1
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Liang Q, Tu B, Cui L. Recombinant T7 RNA polymerase production using ClearColi BL21(DE3) and animal-free media for in vitro transcription. Appl Microbiol Biotechnol 2024; 108:41. [PMID: 38180552 DOI: 10.1007/s00253-023-12939-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024]
Abstract
In vitro transcription (IVT) using T7 RNA polymerase (RNAP) is integral to RNA research, yet producing this enzyme in E. coli presents challenges regarding endotoxins and animal-sourced toxins. This study demonstrates the viable production and characterization of T7 RNAP using ClearColi BL21(DE3) (an endotoxin-free E. coli strain) and animal-free media. Compared to BL21(DE3) with animal-free medium, soluble T7 RNAP expression is ~50% lower in ClearColi BL21(DE3). Optimal soluble T7 RNAP expression in flask fermentation is achieved through the design of experiments (DoE). Specification and functional testing showed that the endotoxin-free T7 RNAP has comparable activity to conventional T7 RNAP. After Ni-NTA purification, endotoxin levels were approximately 109-fold lower than T7 RNAP from BL21(DE3) with animal-free medium. Furthermore, a full factorial DoE created an optimal IVT system that maximized mRNA yield from the endotoxin-free and animal-free T7 RNAP. This work addresses critical challenges in recombinant T7 RNAP production through innovative host and medium combinations, avoided endotoxin risks and animal-derived toxins. Together with an optimized IVT reaction system, this study represents a significant advance for safe and reliable reagent manufacturing and RNA therapeutics. KEY POINTS: • Optimized IVT system maximizes mRNA yields, enabling the synthesis of long RNAs. • Novel production method yields endotoxin-free and animal-free T7 RNAP. • The T7 RNAP has equivalent specifications and function to conventional T7 RNAP.
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Affiliation(s)
- Qianying Liang
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou, 213164, Jiangsu Province, China
| | - Bowen Tu
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu Province, China
| | - Lun Cui
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou, 213164, Jiangsu Province, China.
- CCZU-JITRI Joint Bio-X Lab, Changzhou AiRiBio Healthcare CO., LTD, Changzhou, 213164, Jiangsu Province, China.
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2
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Wanyu Z, Dongling N, Yae Z, Lianying J, Chenglin G, Rong C, Li H. Prokaryotic expression of DFP1 and DFP2 in Dermatophagoides farinae and their responses to temperature stress. Gene 2024; 927:148661. [PMID: 38871034 DOI: 10.1016/j.gene.2024.148661] [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: 03/18/2024] [Revised: 05/29/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
The functions of highly expressed genes DFP1 and DFP2 in Dermatophagoides farinae remain unknown. DFP1 and DFP2 have been abundantly annotated and were up-regulated under temperature stress at 43 °C and -10 °C in our previous RNA-seq study, indicating that DFP1 and DFP2 may have temperature stress response function. Here, we amplified, cloned, and sequenced to obtain the complete coding sequences of DFP1 and DFP2 and predicted their protein characteristics using bioinformatics analysis. Then, prokaryotic expression systems were constructed and found that DFP1 was expressed in Escherichia coli Rosetta-gami 2 (DE3) but not BL21 (DE3); DFP2 was expressed in both BL21 (DE3) and Rosetta-gami 2 (DE3), with higher expression in BL21 (DE3). Finally, the growth curves of bacteria were drawn and indicated that the DFP1- and DFP2-pET32a carrying recombinant bacteria grew better than the respectiveonly pET32a carrying control bacteria after heat and cold stress. This study confirms for the first time that DFP1 and DFP2 respond to temperature stress at the protein level. The constructed prokaryotic expression systems will provide an experimental foundation for future antibody preparation for western blotting detection to confirm the temperature-stress response functions of DFP1 and DFP2.
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Affiliation(s)
- Zhang Wanyu
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Niu Dongling
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China; Clinical Laboratory Center, Xi'an People's Hospital, Xi'an Fourth Hospital, Affiliated People's Hospital of Northwest University, Xi'an 710004, China
| | - Zhao Yae
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Jiao Lianying
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Guan Chenglin
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Chai Rong
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Hu Li
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
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3
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Grafakou A, Mosterd C, de Waal PP, van Rijswijck IMH, van Peij NNME, Mahony J, van Sinderen D. Functional and practical insights into three lactococcal antiphage systems. Appl Environ Microbiol 2024; 90:e0112024. [PMID: 39136492 PMCID: PMC11409693 DOI: 10.1128/aem.01120-24] [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: 06/07/2024] [Accepted: 07/21/2024] [Indexed: 09/19/2024] Open
Abstract
The persistent challenge of phages in dairy fermentations requires the development of starter cultures with enhanced phage resistance. Recently, three plasmid-encoded lactococcal antiphage systems, named Rhea, Aristaios, and Kamadhenu, were discovered. These systems were found to confer high levels of resistance against various Skunavirus members. In the present study, their effectiveness against phage infection was confirmed in milk-based medium, thus validating their potential to ensure reliable dairy fermentations. We furthermore demonstrated that Rhea and Kamadhenu do not directly hinder phage genome replication, transcription, or associated translation. Conversely, Aristaios was found to interfere with phage transcription. Two of the antiphage systems are encoded on pMRC01-like conjugative plasmids, and the Kamadhenu-encoding plasmid was successfully transferred by conjugation to three lactococcal strains, each of which acquired substantially enhanced phage resistance against Skunavirus members. Such advances in our knowledge of the lactococcal phage resistome and the possibility of mobilizing these protective functions to bolster phage protection in sensitive strains provide practical solutions to the ongoing phage problem in industrial food fermentations.IMPORTANCEIn the current study, we characterized and evaluated the mechanistic diversity of three recently described, plasmid-encoded lactococcal antiphage systems. These systems were found to confer high resistance against many members of the most prevalent and problematic lactococcal phage genus, rendering them of particular interest to the dairy industry, where persistent phage challenge requires the development of starter cultures with enhanced phage resistance characteristics. Our acquired knowledge highlights that enhanced understanding of lactococcal phage resistance systems and their encoding plasmids can provide rational and effective solutions to the enduring issue of phage infections in dairy fermentation facilities.
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Affiliation(s)
- Andriana Grafakou
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Cas Mosterd
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul P. de Waal
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft, the Netherlands
| | | | - Noël N. M. E. van Peij
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft, the Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
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4
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Nakamura M, Akada R. Blending of selected yeast extract and peptone for inducible and constitutive protein production in Escherichia coli using the pET system. J Biosci Bioeng 2024:S1389-1723(24)00255-X. [PMID: 39251381 DOI: 10.1016/j.jbiosc.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/11/2024]
Abstract
pET vectors allow inducible expression of recombinant proteins in Escherichia coli. In this system, isopropyl β-d-1-thiogalactopyranoside (IPTG) drives lacUV5 promoter to produce T7 RNA polymerase, simultaneously releasing the suppression of T7lac promoter. T7 RNA polymerase then strongly transcribes the target gene. A lac repressor encoded by lacI in the vector represses the promoters. Despite stringent repression and inducible expression achieved with the pET system, unexpected leaky expression can occur without IPTG induction. Here, by evaluating leaky expression in recombinant cells cultured in various Luria-Bertani (LB) media, prepared using yeast extract and peptone from different suppliers, as well as in five commercial premix-LB media, we confirmed the presence of unknown lac inducers in LB. To explore these inducers, we examined E. coli growth in media comprising yeast extract or peptone. At 4% concentration, five commercial yeast extract and six peptone samples individually allowed E. coli growth equivalent to that in LB medium. We determined the luciferase activity of the luxCDABE operon in the pET vector under these conditions. The presence of different concentrations of inducers was detected in both the yeast extract and peptone. Furthermore, we blended yeast extract and peptone with low or high concentrations of lac inducers. The low-expression blend, used as a basal medium before IPTG addition, allowed leak-free, tightly controlled expression. The high-expression blend was used for constitutive high-expression and pET induction with the basal medium, in lieu of IPTG. These blended media can be used for well-controlled inducible and constitutive expression using the pET system.
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Affiliation(s)
- Mikiko Nakamura
- Department of Instrumental Analysis, Research Center for Advanced Science and Technology, Shinshu University, Matsumoto 390-8621, Japan; Renaissance Center for Applied Microbiology, Shinshu University, Nagano 380-8553, Japan.
| | - Rinji Akada
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8511, Japan
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5
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Charbonneau AA, Reicks EJ, Cambria JF, Inman J, Danley D, Shockley EA, Davion R, Salgado I, Norton EG, Corbett LJ, Hanacek LE, Jensen JG, Kibodeaux MA, Kirkpatrick TK, Rausch KM, Roth SR, West B, Wilson KE, Lawrence CM, Cloninger MJ. CUREs for high-level Galectin-3 expression. Protein Expr Purif 2024; 221:106516. [PMID: 38801985 DOI: 10.1016/j.pep.2024.106516] [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: 02/06/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 05/29/2024]
Abstract
Galectins are a large and diverse protein family defined by the presence of a carbohydrate recognition domain (CRD) that binds β-galactosides. They play important roles in early development, tissue regeneration, immune homeostasis, pathogen recognition, and cancer. In many cases, studies that examine galectin biology and the effect of manipulating galectins are aided by, or require the ability to express and purify, specific members of the galectin family. In many cases, E. coli is employed as a heterologous expression system, and galectin expression is induced with isopropyl β-galactoside (IPTG). Here, we show that galectin-3 recognizes IPTG with micromolar affinity and that as IPTG induces expression, newly synthesized galectin can bind and sequester cytosolic IPTG, potentially repressing further expression. To circumvent this putative inhibitory feedback loop, we utilized an autoinduction protocol that lacks IPTG, leading to significantly increased yields of galectin-3. Much of this work was done within the context of a course-based undergraduate research experience, indicating the ease and reproducibility of the resulting expression and purification protocols.
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Affiliation(s)
| | - Elizabeth J Reicks
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - John F Cambria
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Jacob Inman
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Daria Danley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Emmie A Shockley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Ravenor Davion
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Isabella Salgado
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Erienne G Norton
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Lucy J Corbett
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Lucy E Hanacek
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Jordan G Jensen
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Marguerite A Kibodeaux
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Tess K Kirkpatrick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Keilen M Rausch
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Samantha R Roth
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Bernadette West
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Kenai E Wilson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Mary J Cloninger
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
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6
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Després PC, Dubé AK, Picard MÈ, Grenier J, Shi R, Landry CR. Compensatory mutations potentiate constructive neutral evolution by gene duplication. Science 2024; 385:770-775. [PMID: 39146405 DOI: 10.1126/science.ado5719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024]
Abstract
The functions of proteins generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicated and evolved a homodimeric enzyme to determine whether and how this could happen. We identified hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when coexpressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate.
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Affiliation(s)
- Philippe C Després
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- PROTEO, Le Regroupement Québécois de Recherche sur la Fonction, L'Ingénierie et les Applications des Protéines, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexandre K Dubé
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- PROTEO, Le Regroupement Québécois de Recherche sur la Fonction, L'Ingénierie et les Applications des Protéines, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- PROTEO, Le Regroupement Québécois de Recherche sur la Fonction, L'Ingénierie et les Applications des Protéines, Université Laval, Québec, QC G1V 0A6, Canada
| | - Jordan Grenier
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- PROTEO, Le Regroupement Québécois de Recherche sur la Fonction, L'Ingénierie et les Applications des Protéines, Université Laval, Québec, QC G1V 0A6, Canada
| | - Rong Shi
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- PROTEO, Le Regroupement Québécois de Recherche sur la Fonction, L'Ingénierie et les Applications des Protéines, Université Laval, Québec, QC G1V 0A6, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- PROTEO, Le Regroupement Québécois de Recherche sur la Fonction, L'Ingénierie et les Applications des Protéines, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada
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7
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Sovic L, Malihan-Yap L, Tóth GS, Siitonen V, Alphand V, Allahverdiyeva Y, Kourist R. Sucrose as an electron source for cofactor regeneration in recombinant Escherichia coli expressing invertase and a Baeyer Villiger monooxygenase. Microb Cell Fact 2024; 23:227. [PMID: 39135032 PMCID: PMC11318132 DOI: 10.1186/s12934-024-02474-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/08/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND The large-scale biocatalytic application of oxidoreductases requires systems for a cost-effective and efficient regeneration of redox cofactors. These represent the major bottleneck for industrial bioproduction and an important cost factor. In this work, co-expression of the genes of invertase and a Baeyer-Villiger monooxygenase from Burkholderia xenovorans to E. coli W ΔcscR and E. coli BL21 (DE3) enabled efficient biotransformation of cyclohexanone to the polymer precursor, ε-caprolactone using sucrose as electron source for regeneration of redox cofactors, at rates comparable to glucose. E. coli W ΔcscR has a native csc regulon enabling sucrose utilization and is deregulated via deletion of the repressor gene (cscR), thus enabling sucrose uptake even at concentrations below 6 mM (2 g L-1). On the other hand, E. coli BL21 (DE3), which is widely used as an expression host does not contain a csc regulon. RESULTS Herein, we show a proof of concept where the co-expression of invertase for both E. coli hosts was sufficient for efficient sucrose utilization to sustain cofactor regeneration in the Baeyer-Villiger oxidation of cyclohexanone. Using E. coli W ΔcscR, a specific activity of 37 U gDCW-1 was obtained, demonstrating the suitability of the strain for recombinant gene co-expression and subsequent whole-cell biotransformation. In addition, the same co-expression cassette was transferred and investigated with E. coli BL21 (DE3), which showed a specific activity of 17 U gDCW- 1. Finally, biotransformation using photosynthetically-derived sucrose from Synechocystis S02 with E. coli W ΔcscR expressing BVMO showed complete conversion of cyclohexanone after 3 h, especially with the strain expressing the invertase gene in the periplasm. CONCLUSIONS Results show that sucrose can be an alternative electron source to drive whole-cell biotransformations in recombinant E. coli strains opening novel strategies for sustainable chemical production.
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Affiliation(s)
- Lucija Sovic
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria
| | - Lenny Malihan-Yap
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria
| | - Gábor Szilveszter Tóth
- Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014, Turku, Finland
| | - Vilja Siitonen
- Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014, Turku, Finland
| | - Véronique Alphand
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014, Turku, Finland
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria.
- ACIB GmbH, 8010, Graz, Austria.
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8
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Pakamwong B, Thongdee P, Kamsri B, Phusi N, Taveepanich S, Chayajarus K, Kamsri P, Punkvang A, Hannongbua S, Sangswan J, Suttisintong K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Leanpolchareanchai J, Spencer J, Mulholland AJ, Pungpo P. Ligand-Based Virtual Screening for Discovery of Indole Derivatives as Potent DNA Gyrase ATPase Inhibitors Active against Mycobacterium tuberculosis and Hit Validation by Biological Assays. J Chem Inf Model 2024; 64:5991-6002. [PMID: 38993154 PMCID: PMC11323271 DOI: 10.1021/acs.jcim.4c00511] [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: 03/25/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Mycobacterium tuberculosis is the single most important global infectious disease killer and a World Health Organization critical priority pathogen for development of new antimicrobials. M. tuberculosis DNA gyrase is a validated target for anti-TB agents, but those in current use target DNA breakage-reunion, rather than the ATPase activity of the GyrB subunit. Here, virtual screening, subsequently validated by whole-cell and enzyme inhibition assays, was applied to identify candidate compounds that inhibit M. tuberculosis GyrB ATPase activity from the Specs compound library. This approach yielded six compounds: four carbazole derivatives (1, 2, 3, and 8), the benzoindole derivative 11, and the indole derivative 14. Carbazole derivatives can be considered a new scaffold for M. tuberculosis DNA gyrase ATPase inhibitors. IC50 values of compounds 8, 11, and 14 (0.26, 0.56, and 0.08 μM, respectively) for inhibition of M. tuberculosis DNA gyrase ATPase activity are 5-fold, 2-fold, and 16-fold better than the known DNA gyrase ATPase inhibitor novobiocin. MIC values of these compounds against growth of M. tuberculosis H37Ra are 25.0, 3.1, and 6.2 μg/mL, respectively, superior to novobiocin (MIC > 100.0 μg/mL). Molecular dynamics simulations of models of docked GyrB:inhibitor complexes suggest that hydrogen bond interactions with GyrB Asp79 are crucial for high-affinity binding of compounds 8, 11, and 14 to M. tuberculosis GyrB for inhibition of ATPase activity. These data demonstrate that virtual screening can identify known and new scaffolds that inhibit both M. tuberculosis DNA gyrase ATPase activity in vitro and growth of M. tuberculosis bacteria.
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Affiliation(s)
- Bongkochawan Pakamwong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Paptawan Thongdee
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Bundit Kamsri
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Naruedon Phusi
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Somjintana Taveepanich
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Kampanart Chayajarus
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Pharit Kamsri
- Division
of Chemistry, Faculty of Science, Nakhon
Phanom University, Nakhon
Phanom 48000, Thailand
| | - Auradee Punkvang
- Division
of Chemistry, Faculty of Science, Nakhon
Phanom University, Nakhon
Phanom 48000, Thailand
| | - Supa Hannongbua
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Bangkok 10900, Thailand
| | - Jidapa Sangswan
- Department
of Biological Science, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Khomson Suttisintong
- National
Nanotechnology Center, NSTDA, 111 Thailand Science Park, Klong
Luang, Pathum Thani 12120, Thailand
| | - Sanya Sureram
- Chulabhorn
Research Institute, Laksi, Bangkok 10210, Thailand
| | - Prasat Kittakoop
- Chulabhorn
Research Institute, Laksi, Bangkok 10210, Thailand
- Program
in Chemical Sciences, Chulabhorn Graduate
Institute, Bangkok 10210, Thailand
- Center
of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and
Innovation, Bangkok 10210, Thailand
| | - Poonpilas Hongmanee
- Division
of Clinical Microbiology, Department of Pathology, Faculty of Medicine,
Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Pitak Santanirand
- Division
of Clinical Microbiology, Department of Pathology, Faculty of Medicine,
Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | | | - James Spencer
- School
of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K.
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Pornpan Pungpo
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
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9
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Yang X, Cao S, Sun H, Deng Y, Zhang X, Li Y, Ma D, Chen H, Li W. The critical roles of the Zn 2Cys 6 transcription factor Fp487 in the development and virulence of Fusarium pseudograminearum: A potential target for Fusarium crown rot control. Microbiol Res 2024; 285:127784. [PMID: 38824820 DOI: 10.1016/j.micres.2024.127784] [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: 02/25/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
Abstract
Fusarium crown rot (FCR) caused by Fusarium pseudograminearum poses a significant threat to wheat production in the Huang-Huai-Hai region of China. However, the pathogenic mechanism of F. pseudograminearum is still poorly understood. Zn2Cys6 transcription factors, which are exclusive to fungi, play pivotal roles in regulating fungal development, drug resistance, pathogenicity, and secondary metabolism. In this study, we present the functional characterization of a Zn2Cys6 transcription factor F. pseudograminearum, designated Fp487. In F. pseudograminearum, Fp487 is shown to be required for mycelial growth through gene knockout and phenotypic analyses. Compared with wild-type CF14047, the ∆Fp487 mutant displayed a slight reduction in growth rate but a significant decrease in conidiogenesis, pathogenicity and 3-acetyl-deoxynivalenol (3AcDON) production. Moreover, the mutant exhibited heightened sensitivity to oxidative and cytomembrane stress. Furthermore, we synthesized dsRNA from the Fp487 gene in vitro, resulting in a reduction in the growth rate of F. pseudograminearum and its virulence on barley leaves through spray-induced gene silencing (SIGS). Notably, this study makes the first instance of inducing the expression of abundant dsRNA from F. pseudograminearum by engineering the Escherichia coli strain HT115 (DE3) and utilizing the SIGS technique to evaluate the virulence effect of dsRNA on F. pseudograminearum. In conclusion, our findings revealed the crucial role of Fp487 in regulating pathogenicity, stress responses, DON production, and conidiogenesis in F. pseudograminearum. Furthermore, Fp487 is a potential RNAi-based target for FCR control.
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Affiliation(s)
- Xiaoyue Yang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Haiyan Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yuanyu Deng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Xin Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yan Li
- Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Dongfang Ma
- Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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10
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Bianchi G, Pessina A, Ami D, Signorelli S, de Divitiis M, Natalello A, Lotti M, Brambilla L, Brocca S, Mangiagalli M. Sustainable production of a biotechnologically relevant β-galactosidase in Escherichia coli cells using crude glycerol and cheese whey permeate. BIORESOURCE TECHNOLOGY 2024; 406:131063. [PMID: 38964512 DOI: 10.1016/j.biortech.2024.131063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/06/2024]
Abstract
Responsible use of natural resources and waste reduction are key concepts in bioeconomy. This study demonstrates that agro-food derived-biomasses from the Italian food industry, such as crude glycerol and cheese whey permeate (CWP), can be combined in a high-density fed-batch culture to produce a recombinant β-galactosidase from Marinomonas sp. ef1 (M-βGal). In a small-scale process (1.5 L) using 250 mL of crude glycerol and 300 mL of lactose-rich CWP, approximately 2000 kU of recombinant M-βGal were successfully produced along with 30 g of galactose accumulated in the culture medium. The purified M-βGal exhibited high hydrolysis efficiency in lactose-rich matrices, with hydrolysis yields of 82 % in skimmed milk at 4 °C and 94 % in CWP at 50 °C, highlighting its biotechnological potential. This approach demonstrates the effective use of crude glycerol and CWP in sustainable and cost-effective high-density Escherichia coli cultures, potentially applicable to recombinant production of various proteins.
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Affiliation(s)
- Greta Bianchi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Samuele Signorelli
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Marcella de Divitiis
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Luca Brambilla
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy.
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy.
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11
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Matos RG, Simmons KJ, Fishwick CWG, McDowall KJ, Arraiano CM. Identification of Ribonuclease Inhibitors for the Control of Pathogenic Bacteria. Int J Mol Sci 2024; 25:8048. [PMID: 39125622 PMCID: PMC11311990 DOI: 10.3390/ijms25158048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 08/12/2024] Open
Abstract
Bacteria are known to be constantly adapting to become resistant to antibiotics. Currently, efficient antibacterial compounds are still available; however, it is only a matter of time until these compounds also become inefficient. Ribonucleases are the enzymes responsible for the maturation and degradation of RNA molecules, and many of them are essential for microbial survival. Members of the PNPase and RNase II families of exoribonucleases have been implicated in virulence in many pathogens and, as such, are valid targets for the development of new antibacterials. In this paper, we describe the use of virtual high-throughput screening (vHTS) to identify chemical compounds predicted to bind to the active sites within the known structures of RNase II and PNPase from Escherichia coli. The subsequent in vitro screening identified compounds that inhibited the activity of these exoribonucleases, with some also affecting cell viability, thereby providing proof of principle for utilizing the known structures of these enzymes in the pursuit of new antibacterials.
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Affiliation(s)
- Rute G. Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Katie J. Simmons
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK;
| | - Colin W. G. Fishwick
- Astbury Centre for Structural Molecular Biology, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, UK;
| | - Kenneth J. McDowall
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK;
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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12
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Johnson AO, Shipman BM, Hunt BC, Learman BS, Brauer AL, Zhou SP, Hageman Blair R, De Nisco NJ, Armbruster CE. Function and contribution of two putative Enterococcus faecalis glycosaminoglycan degrading enzymes to bacteremia and catheter-associated urinary tract infection. Infect Immun 2024; 92:e0019924. [PMID: 38842305 PMCID: PMC11238560 DOI: 10.1128/iai.00199-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
Enterococcus faecalis is a common cause of healthcare-acquired bloodstream infections and catheter-associated urinary tract infections (CAUTIs) in both adults and children. Treatment of E. faecalis infection is frequently complicated by multi-drug resistance. Based on protein homology, E. faecalis encodes two putative hyaluronidases, EF3023 (HylA) and EF0818 (HylB). In other Gram-positive pathogens, hyaluronidases have been shown to contribute to tissue damage and immune evasion, but the function in E. faecalis has yet to be explored. Here, we show that both hylA and hylB contribute to E. faecalis pathogenesis. In a CAUTI model, ΔhylA exhibited defects in bladder colonization and dissemination to the bloodstream, and ΔhylB exhibited a defect in kidney colonization. Furthermore, a ΔhylAΔhylB double mutant exhibited a severe colonization defect in a model of bacteremia while the single mutants colonized to a similar level as the wild-type strain, suggesting potential functional redundancy within the bloodstream. We next examined enzymatic activity, and demonstrate that HylB is capable of digesting both hyaluronic acid (HA) and chondroitin sulfate in vitro, while HylA exhibits only a very modest activity against heparin. Importantly, HA degradation by HylB provided a modest increase in cell density during the stationary phase and also contributed to dampening of lipopolysaccharide-mediated NF-κB activation. Overall, these data demonstrate that glycosaminoglycan degradation is important for E. faecalis pathogenesis in the urinary tract and during bloodstream infection.
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Affiliation(s)
- Alexandra O Johnson
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Braden M Shipman
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Benjamin C Hunt
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Brian S Learman
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Aimee L Brauer
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Serena P Zhou
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Rachael Hageman Blair
- Department of Biostatistics, School of Public Health and Health Professions, State University of New York at Buffalo, Buffalo, New York, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chelsie E Armbruster
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
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13
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Zott B, Nästle L, Grienberger C, Unger F, Knauer MM, Wolf C, Keskin-Dargin A, Feuerbach A, Busche MA, Skerra A, Konnerth A. β-amyloid monomer scavenging by an anticalin protein prevents neuronal hyperactivity in mouse models of Alzheimer's Disease. Nat Commun 2024; 15:5819. [PMID: 38987287 PMCID: PMC11237084 DOI: 10.1038/s41467-024-50153-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/02/2024] [Indexed: 07/12/2024] Open
Abstract
Hyperactivity mediated by synaptotoxic β-amyloid (Aβ) oligomers is one of the earliest forms of neuronal dysfunction in Alzheimer's disease. In the search for a preventive treatment strategy, we tested the effect of scavenging Aβ peptides before Aβ plaque formation. Using in vivo two-photon calcium imaging and SF-iGluSnFR-based glutamate imaging in hippocampal slices, we demonstrate that an Aβ binding anticalin protein (Aβ-anticalin) can suppress early neuronal hyperactivity and synaptic glutamate accumulation in the APP23xPS45 mouse model of β-amyloidosis. Our results suggest that the sole targeting of Aβ monomers is sufficient for the hyperactivity-suppressing effect of the Aβ-anticalin at early disease stages. Biochemical and neurophysiological analyses indicate that the Aβ-anticalin-dependent depletion of naturally secreted Aβ monomers interrupts their aggregation to neurotoxic oligomers and, thereby, reverses early neuronal and synaptic dysfunctions. Thus, our results suggest that Aβ monomer scavenging plays a key role in the repair of neuronal function at early stages of AD.
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Affiliation(s)
- Benedikt Zott
- Institute of Neuroscience, Technical University of Munich, Munich, Germany.
- Department of Neuroradiology, MRI hospital of the Technical University of Munich, Munich, Germany.
- TUM Institute for Advanced Study, Garching, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Lea Nästle
- Chair of Biological Chemistry, Technical University of Munich, Freising, Germany
| | - Christine Grienberger
- Institute of Neuroscience, Technical University of Munich, Munich, Germany
- Department of Biology and Volen National Center of Complex Systems, Brandeis University, Waltham, MA, USA
| | - Felix Unger
- Institute of Neuroscience, Technical University of Munich, Munich, Germany
- Department of Neuroradiology, MRI hospital of the Technical University of Munich, Munich, Germany
- TUM Institute for Advanced Study, Garching, Germany
| | - Manuel M Knauer
- Institute of Neuroscience, Technical University of Munich, Munich, Germany
| | - Christian Wolf
- Institute of Neuroscience, Technical University of Munich, Munich, Germany
- Department of Neuroradiology, MRI hospital of the Technical University of Munich, Munich, Germany
| | | | - Anna Feuerbach
- Chair of Biological Chemistry, Technical University of Munich, Freising, Germany
| | - Marc Aurel Busche
- Institute of Neuroscience, Technical University of Munich, Munich, Germany
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Arne Skerra
- Chair of Biological Chemistry, Technical University of Munich, Freising, Germany.
| | - Arthur Konnerth
- Institute of Neuroscience, Technical University of Munich, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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14
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DasGupta S. Synthetic antibodies for accelerated RNA crystallography. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1869. [PMID: 39187256 DOI: 10.1002/wrna.1869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/04/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024]
Abstract
RNA structure is crucial to a wide range of cellular processes. The intimate relationship between macromolecular structure and function necessitates the determination of high-resolution structures of functional RNA molecules. X-ray crystallography is the predominant technique used for macromolecular structure determination; however, solving RNA structures has been more challenging than their protein counterparts, as reflected in their poor representation in the Protein Data Bank (<1%). Antibody-assisted RNA crystallography is a relatively new technique that promises to accelerate RNA structure determination by employing synthetic antibodies (Fabs) as crystallization chaperones that are specifically raised against target RNAs. Antibody chaperones facilitate the formation of ordered crystal lattices by minimizing RNA flexibility and replacing unfavorable RNA-RNA contacts with contacts between chaperone molecules. Atomic coordinates of these antibody fragments can also be used as search models to obtain phase information during structure determination. Antibody-assisted RNA crystallography has enabled the structure determination of 15 unique RNA targets, including 11 in the last 6 years. In this review, I cover the historical development of antibody fragments as crystallization chaperones and their application to diverse RNA targets. I discuss how the first structures of antibody-RNA complexes informed the design of second-generation antibodies and led to the development of portable crystallization modules that have greatly reduced the uncertainties associated with RNA crystallography. Finally, I outline unexplored avenues that can increase the impact of this technology in structural biology research and discuss potential applications of antibodies as affinity reagents for interrogating RNA biology outside of their use in crystallography. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
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15
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Aliakbari M, Karkhane AA. In vivo cloning of PCR product via site-specific recombination in Escherichia coli. Appl Microbiol Biotechnol 2024; 108:400. [PMID: 38951186 PMCID: PMC11217044 DOI: 10.1007/s00253-024-13239-7] [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: 03/25/2024] [Revised: 06/02/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
Over the past years, several methods have been developed for gene cloning. Choosing a cloning strategy depends on various factors, among which simplicity and affordability have always been considered. The aim of this study, on the one hand, is to simplify gene cloning by skipping in vitro assembly reactions and, on the other hand, to reduce costs by eliminating relatively expensive materials. We investigated a cloning system using Escherichia coli harboring two plasmids, pLP-AmpR and pScissors-CmR. The pLP-AmpR contains a landing pad (LP) consisting of two genes (λ int and λ gam) that allow the replacement of the transformed linear DNA using site-specific recombination. After the replacement process, the inducible expressing SpCas9 and specific sgRNA from the pScissors-CmR (CRISPR/Cas9) vector leads to the removal of non-recombinant pLP-AmpR plasmids. The function of LP was explored by directly transforming PCR products. The pScissors-CmR plasmid was evaluated for curing three vectors, including the origins of pBR322, p15A, and pSC101. Replacing LP with a PCR product and fast-eradicating pSC101 origin-containing vectors was successful. Recombinant colonies were confirmed following gene replacement and plasmid curing processes. The results made us optimistic that this strategy may potentially be a simple and inexpensive cloning method. KEY POINTS: •The in vivo cloning was performed by replacing the target gene with the landing pad. •Fast eradication of non-recombinant plasmids was possible by adapting key vectors. •This strategy is not dependent on in vitro assembly reactions and expensive materials.
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Affiliation(s)
- Moein Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Asghar Karkhane
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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16
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Del Rio Flores A, Zhai R, Zhang W. Isonitrile biosynthesis by non-heme iron(II)-dependent oxidases/decarboxylases. Methods Enzymol 2024; 704:143-172. [PMID: 39300646 PMCID: PMC11424024 DOI: 10.1016/bs.mie.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The isonitrile group is a compact, electron-rich moiety coveted for its commonplace as a building block and bioorthogonal functionality in synthetic chemistry and chemical biology. Hundreds of natural products containing an isonitrile group with intriguing bioactive properties have been isolated from diverse organisms. Our recent discovery of a conserved biosynthetic gene cluster in some Actinobacteria species highlighted a novel enzymatic pathway to isonitrile formation involving a non-heme iron(II) and α-ketoglutarate-dependent dioxygenase. Here, we focus this chapter on recent advances in understanding and probing the biosynthetic machinery for isonitrile synthesis by non-heme iron(II) and α-ketoglutarate-dependent dioxygenases. We will begin by describing how to harness isonitrile enzymatic machinery through heterologous expression, purification, synthetic strategies, and in vitro biochemical/kinetic characterization. We will then describe a generalizable strategy to probe the mechanism for isonitrile formation by combining various spectroscopic methods. The chapter will also cover strategies to study other enzyme homologs by implementing coupled assays using biosynthetic pathway enzymes. We will conclude this chapter by addressing current challenges and future directions in understanding and engineering isonitrile synthesis.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States.
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17
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Ishii M, Matsumoto Y, Yamada T, Uga H, Katada T, Ohata S. Targeting dermatophyte Cdc42 and Rac GTPase signaling to hinder hyphal elongation and virulence. iScience 2024; 27:110139. [PMID: 38952678 PMCID: PMC11215307 DOI: 10.1016/j.isci.2024.110139] [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: 11/07/2023] [Revised: 04/18/2024] [Accepted: 05/27/2024] [Indexed: 07/03/2024] Open
Abstract
The development of antifungal drugs requires novel molecular targets due to limited treatment options and drug resistance. Through chemical screening and establishment of a novel genetic technique to repress gene expression in Trichophyton rubrum, the primary causal fungus of dermatophytosis, we demonstrated that fungal Cdc42 and Rac GTPases are promising antifungal drug targets. Chemical inhibitors of these GTPases impair hyphal formation, which is crucial for growth and virulence in T. rubrum. Conditional repression of Cdc24, a guanine nucleotide exchange factor for Cdc42 and Rac, led to hyphal growth defects, abnormal cell morphology, and cell death. EHop-016 inhibited the promotion of the guanine nucleotide exchange reaction in Cdc42 and Rac by Cdc24 as well as germination and growth on the nail fragments of T. rubrum and improved animal survival in an invertebrate infection model of T. rubrum. Our results provide a novel antifungal therapeutic target and a potential lead compound.
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Affiliation(s)
- Masaki Ishii
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, Tokyo 202-8585, Japan
| | - Yasuhiko Matsumoto
- Department of Microbiology, Meiji Pharmaceutical University, 2–522–1 Noshio, Kiyose, Tokyo 204–8588, Japan
| | - Tsuyoshi Yamada
- Teikyo University Institute of Medical Mycology, Teikyo University, Hachioji, Tokyo 192-0395, Japan
- Asia International Institute of Infectious Disease Control, Teikyo University, Tokyo 173-0003, Japan
| | - Hideko Uga
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, Tokyo 202-8585, Japan
| | - Toshiaki Katada
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, Tokyo 202-8585, Japan
| | - Shinya Ohata
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, Tokyo 202-8585, Japan
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18
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März C, Nölting S, Wollenschläger L, Pühler A, Kalinowski J. Role of MalQ Enzyme in a Reconstructed Maltose/Maltodextrin Pathway in Actinoplanes sp. SE50/110. Microorganisms 2024; 12:1221. [PMID: 38930603 PMCID: PMC11205506 DOI: 10.3390/microorganisms12061221] [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: 05/28/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The pseudotetrasaccharide acarbose, produced by Actinoplanes sp. SE50/110, is a relevant secondary metabolite used in diabetes type II medication. Although maltose plays a crucial role in acarbose biosynthesis, the understanding of the maltose/maltodextrin metabolism and its involvement in acarbose production is at an early stage. Here, we reconstructed the predicted maltose-maltodextrin pathway that involves four enzymes AmlE, MalZ, MalP, and MalQ. An investigation of enzyme activities was conducted through in vitro assays, leading to an expansion of previously postulated substrate spectra. The maltose-induced α-glucosidase AmlE is noteworthy for its high hydrolysis rate of linear α-1,4-glucans, and its capability to hydrolyze various glycosidic bonds. The predicted maltodextrin glucosidase MalZ showed slow hydrolysis activity on linear α-glucans, but it was resistant to acarbose and capable of releasing glucose from acarbose. AmlE compensates for the low activity of MalZ to ensure glucose supply. We determined the enzyme activity of MalP and its dual function as maltodextrin and glycogen phosphorylase. The 4-α-glucanotransferase MalQ plays a central role in the maltose/maltodextrin metabolism, alongside MalP. This study confirmed the simultaneous degradation and synthesis of long-chain α-glucans. The product distribution showed that with an increasing number of glycosidic bonds, less glucose is formed. We found that MalQ, like its sequence homolog AcbQ from the acarbose biosynthetic gene cluster, is involved in the formation of elongated acarviosyl metabolites. However, MalQ does not participate in the elongation of acarbose 7-phosphate, which is likely the more readily available acceptor molecule in vivo. Accordingly, MalQ is not involved in the formation of acarviosyl impurities in Actinoplanes sp. SE50/110.
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Affiliation(s)
- Camilla März
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; (C.M.); (S.N.); (L.W.)
| | - Sophia Nölting
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; (C.M.); (S.N.); (L.W.)
| | - Lars Wollenschläger
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; (C.M.); (S.N.); (L.W.)
| | - Alfred Pühler
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; (C.M.); (S.N.); (L.W.)
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19
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Bennett ZD, Brunold TC. Non-standard amino acid incorporation into thiol dioxygenases. Methods Enzymol 2024; 703:121-145. [PMID: 39260993 PMCID: PMC11391102 DOI: 10.1016/bs.mie.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Thiol dioxygenases (TDOs) are non‑heme Fe(II)‑dependent enzymes that catalyze the O2-dependent oxidation of thiol substrates to their corresponding sulfinic acids. Six classes of TDOs have thus far been identified and two, cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO), are found in eukaryotes. All TDOs belong to the cupin superfamily of enzymes, which share a common β‑barrel fold and two cupin motifs: G(X)5HXH(X)3-6E(X)6G and G(X)5-7PXG(X)2H(X)3N. Crystal structures of TDOs revealed that these enzymes contain a relatively rare, neutral 3‑His iron‑binding facial triad. Despite this shared metal-binding site, TDOs vary greatly in their secondary coordination spheres. Site‑directed mutagenesis has been used extensively to explore the impact of changes in secondary sphere residues on substrate specificity and enzymatic efficiency. This chapter summarizes site-directed mutagenesis studies of eukaryotic TDOs, focusing on the tools and practicality of non‑standard amino acid incorporation.
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Affiliation(s)
- Zachary D Bennett
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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20
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van der Sijs A, Visser T, Moerman P, Folkers G, Kegel W. Broccoli aptamer allows quantitative transcription regulation studies in vitro. PLoS One 2024; 19:e0304677. [PMID: 38870160 PMCID: PMC11175446 DOI: 10.1371/journal.pone.0304677] [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: 02/16/2024] [Accepted: 05/15/2024] [Indexed: 06/15/2024] Open
Abstract
Quantitative transcription regulation studies in vivo and in vitro often make use of reporter proteins. Here we show that using Broccoli aptamers, quantitative study of transcription in various regulatory scenarios is possible without a translational step. To explore the method we studied several regulatory scenarios that we analyzed using thermodynamic occupancy-based models, and found excellent agreement with previous studies. In the next step we show that non-coding DNA can have a dramatic effect on the level of transcription, similar to the influence of the lac repressor with a strong affinity to operator sites. Finally, we point out the limitations of the method in terms of delay times coupled to the folding of the aptamer. We conclude that the Broccoli aptamer is suitable for quantitative transcription measurements.
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Affiliation(s)
- Amanda van der Sijs
- Van ’t Hoff Laboratory for Physical and Colloidal Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Thomas Visser
- Van ’t Hoff Laboratory for Physical and Colloidal Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Pepijn Moerman
- Self-Organizing Soft Matter, Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Gert Folkers
- Utrecht NMR Group, Bijvoet Centre fo Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Willem Kegel
- Van ’t Hoff Laboratory for Physical and Colloidal Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
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21
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Hart MT, Rom JS, Le Breton Y, Hause LL, Belew AT, El-Sayed NM, McIver KS. The Streptococcus pyogenes stand-alone regulator RofA exhibits characteristics of a PRD-containing virulence regulator. Infect Immun 2024; 92:e0008324. [PMID: 38712951 PMCID: PMC11237776 DOI: 10.1128/iai.00083-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Streptococcus pyogenes [group A streptococcus (GAS)] is a human pathogen capable of infecting diverse tissues. To successfully infect these sites, GAS must detect available nutrients and adapt accordingly. The phosphoenolpyruvate transferase system (PTS) mediates carbohydrate uptake and metabolic gene regulation to adapt to the nutritional environment. Regulation by the PTS can occur through phosphorylation of transcriptional regulators at conserved PTS-regulatory domains (PRDs). GAS has several PRD-containing stand-alone regulators with regulons encoding both metabolic genes and virulence factors [PRD-containing virulence regulators (PCVRs)]. One is RofA, which regulates the expression of virulence genes in multiple GAS serotypes. It was hypothesized that RofA is phosphorylated by the PTS in response to carbohydrate levels to coordinate virulence gene expression. In this study, the RofA regulon of M1T1 strain 5448 was determined using RNA sequencing. Two operons were consistently differentially expressed across growth in the absence of RofA; the pilus operon was downregulated, and the capsule operon was upregulated. This correlated with increased capsule production and decreased adherence to keratinocytes. Purified RofA-His was phosphorylated in vitro by PTS proteins EI and HPr, and phosphorylated RofA-FLAG was detected in vivo when GAS was grown in low-glucose C medium. Phosphorylated RofA was not observed when C medium was supplemented 10-fold with glucose. Mutations of select histidine residues within the putative PRDs contributed to the in vivo phosphorylation of RofA, although phosphorylation of RofA was still observed, suggesting other phosphorylation sites exist in the protein. Together, these findings support the hypothesis that RofA is a PCVR that may couple sugar metabolism with virulence regulation.
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Affiliation(s)
- Meaghan T Hart
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
| | - Joseph S Rom
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
| | - Yoann Le Breton
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
| | - Lara L Hause
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
| | - Ashton T Belew
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Najib M El-Sayed
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Kevin S McIver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
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22
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Brudenell EL, Pohare MB, Zafred D, Phipps J, Hornsby HR, Darby JF, Dai J, Liggett E, Cain KM, Barran PE, de Silva TI, Sayers JR. Efficient overexpression and purification of severe acute respiratory syndrome coronavirus 2 nucleocapsid proteins in Escherichia coli. Biochem J 2024; 481:669-682. [PMID: 38713013 PMCID: PMC11346444 DOI: 10.1042/bcj20240019] [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: 01/22/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
The fundamental biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and its potential application as a vaccine component have received considerable attention since the outbreak of the Covid19 pandemic in late 2019. Here we report the scalable expression and purification of soluble, immunologically active, SARS-CoV-2 Ncap in Escherichia coli. Codon-optimised synthetic genes encoding the original Ncap sequence and four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into an inducible expression vector carrying a regulated bacteriophage T5 synthetic promoter controlled by lac operator binding sites. The constructs were used to express Ncap proteins and protocols developed which allow efficient production of purified Ncap with yields of over 200 mg per litre of culture media. These proteins were deployed in ELISA assays to allow comparison of their responses to human sera. Our results suggest that there was no detectable difference between the 6His-tagged and untagged original Ncap proteins but there may be a slight loss of sensitivity of sera to other Ncap isolates.
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Affiliation(s)
- Emma L. Brudenell
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Manoj B. Pohare
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Domen Zafred
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Janine Phipps
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Hailey R. Hornsby
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - John F. Darby
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Junxiao Dai
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Ellen Liggett
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Kathleen M. Cain
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Thushan I. de Silva
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Jon R. Sayers
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
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23
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Curry E, Muir G, Qu J, Kis Z, Hulley M, Brown A. Engineering an Escherichia coli based in vivo mRNA manufacturing platform. Biotechnol Bioeng 2024; 121:1912-1926. [PMID: 38419526 DOI: 10.1002/bit.28684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Synthetic mRNA is currently produced in standardized in vitro transcription systems. However, this one-size-fits-all approach has associated drawbacks in supply chain shortages, high reagent costs, complex product-related impurity profiles, and limited design options for molecule-specific optimization of product yield and quality. Herein, we describe for the first time development of an in vivo mRNA manufacturing platform, utilizing an Escherichia coli cell chassis. Coordinated mRNA, DNA, cell and media engineering, primarily focussed on disrupting interactions between synthetic mRNA molecules and host cell RNA degradation machinery, increased product yields >40-fold compared to standard "unengineered" E. coli expression systems. Mechanistic dissection of cell factory performance showed that product mRNA accumulation levels approached theoretical limits, accounting for ~30% of intracellular total RNA mass, and that this was achieved via host-cell's reallocating biosynthetic capacity away from endogenous RNA and cell biomass generation activities. We demonstrate that varying sized functional mRNA molecules can be produced in this system and subsequently purified. Accordingly, this study introduces a new mRNA production technology, expanding the solution space available for mRNA manufacturing.
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Affiliation(s)
- Edward Curry
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - George Muir
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Jixin Qu
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Zoltán Kis
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | - Adam Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
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24
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Gonçalves AAM, Ribeiro AJ, Resende CAA, Couto CAP, Gandra IB, Dos Santos Barcelos IC, da Silva JO, Machado JM, Silva KA, Silva LS, Dos Santos M, da Silva Lopes L, de Faria MT, Pereira SP, Xavier SR, Aragão MM, Candida-Puma MA, de Oliveira ICM, Souza AA, Nogueira LM, da Paz MC, Coelho EAF, Giunchetti RC, de Freitas SM, Chávez-Fumagalli MA, Nagem RAP, Galdino AS. Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis. Microb Cell Fact 2024; 23:145. [PMID: 38778337 PMCID: PMC11110257 DOI: 10.1186/s12934-024-02418-w] [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: 01/31/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Recombinant multiepitope proteins (RMPs) are a promising alternative for application in diagnostic tests and, given their wide application in the most diverse diseases, this review article aims to survey the use of these antigens for diagnosis, as well as discuss the main points surrounding these antigens. RMPs usually consisting of linear, immunodominant, and phylogenetically conserved epitopes, has been applied in the experimental diagnosis of various human and animal diseases, such as leishmaniasis, brucellosis, cysticercosis, Chagas disease, hepatitis, leptospirosis, leprosy, filariasis, schistosomiasis, dengue, and COVID-19. The synthetic genes for these epitopes are joined to code a single RMP, either with spacers or fused, with different biochemical properties. The epitopes' high density within the RMPs contributes to a high degree of sensitivity and specificity. The RMPs can also sidestep the need for multiple peptide synthesis or multiple recombinant proteins, reducing costs and enhancing the standardization conditions for immunoassays. Methods such as bioinformatics and circular dichroism have been widely applied in the development of new RMPs, helping to guide their construction and better understand their structure. Several RMPs have been expressed, mainly using the Escherichia coli expression system, highlighting the importance of these cells in the biotechnological field. In fact, technological advances in this area, offering a wide range of different strains to be used, make these cells the most widely used expression platform. RMPs have been experimentally used to diagnose a broad range of illnesses in the laboratory, suggesting they could also be useful for accurate diagnoses commercially. On this point, the RMP method offers a tempting substitute for the production of promising antigens used to assemble commercial diagnostic kits.
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Affiliation(s)
- Ana Alice Maia Gonçalves
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Anna Julia Ribeiro
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Carlos Ananias Aparecido Resende
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Carolina Alves Petit Couto
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Isadora Braga Gandra
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Isabelle Caroline Dos Santos Barcelos
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Jonatas Oliveira da Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Juliana Martins Machado
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Kamila Alves Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Líria Souza Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Michelli Dos Santos
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Lucas da Silva Lopes
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Mariana Teixeira de Faria
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Sabrina Paula Pereira
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Sandra Rodrigues Xavier
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Matheus Motta Aragão
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Mayron Antonio Candida-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | | | - Amanda Araujo Souza
- Biophysics Laboratory, Institute of Biological Sciences, Department of Cell Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Lais Moreira Nogueira
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Mariana Campos da Paz
- Bioactives and Nanobiotechnology Laboratory, Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Eduardo Antônio Ferraz Coelho
- Postgraduate Program in Health Sciences, Infectious Diseases and Tropical Medicine, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, 30130-100, Brazil
| | - Rodolfo Cordeiro Giunchetti
- Laboratory of Biology of Cell Interactions, National Institute of Science and Technology on Tropical Diseases (INCT-DT), Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Sonia Maria de Freitas
- Biophysics Laboratory, Institute of Biological Sciences, Department of Cell Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | - Ronaldo Alves Pinto Nagem
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Alexsandro Sobreira Galdino
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil.
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25
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Khan H, Paul P, Goar H, Bamniya B, Baid N, Sarkar D. Mycobacterium tuberculosis PhoP integrates stress response to intracellular survival by regulating cAMP level. eLife 2024; 13:RP92136. [PMID: 38739431 PMCID: PMC11090507 DOI: 10.7554/elife.92136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
Survival of Mycobacterium tuberculosis within the host macrophages requires the bacterial virulence regulator PhoP, but the underlying reason remains unknown. 3',5'-Cyclic adenosine monophosphate (cAMP) is one of the most widely used second messengers, which impacts a wide range of cellular responses in microbial pathogens including M. tuberculosis. Herein, we hypothesized that intra-bacterial cAMP level could be controlled by PhoP since this major regulator plays a key role in bacterial responses against numerous stress conditions. A transcriptomic analysis reveals that PhoP functions as a repressor of cAMP-specific phosphodiesterase (PDE) Rv0805, which hydrolyzes cAMP. In keeping with these results, we find specific recruitment of the regulator within the promoter region of rv0805 PDE, and absence of phoP or ectopic expression of rv0805 independently accounts for elevated PDE synthesis, leading to the depletion of intra-bacterial cAMP level. Thus, genetic manipulation to inactivate PhoP-rv0805-cAMP pathway decreases cAMP level, stress tolerance, and intracellular survival of the bacillus.
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Affiliation(s)
- Hina Khan
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Partha Paul
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Harsh Goar
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Bhanwar Bamniya
- CSIR, Institute of Microbial TechnologyChandigarhIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Navin Baid
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Dibyendu Sarkar
- CSIR, Institute of Microbial TechnologyChandigarhIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
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26
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Schoenmakers LLJ, den Uijl MJ, Postma JL, van den Akker TAP, Huck WTS, Driessen AJM. SecYEG-mediated translocation in a model synthetic cell. Synth Biol (Oxf) 2024; 9:ysae007. [PMID: 38807757 PMCID: PMC11131593 DOI: 10.1093/synbio/ysae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Giant unilamellar vesicles (GUVs) provide a powerful model compartment for synthetic cells. However, a key challenge is the incorporation of membrane proteins that allow for transport, energy transduction, compartment growth and division. Here, we have successfully incorporated the membrane protein complex SecYEG-the key bacterial translocase that is essential for the incorporation of newly synthesized membrane proteins-in GUVs. Our method consists of fusion of small unilamellar vesicles containing reconstituted SecYEG into GUVs, thereby forming SecGUVs. These are suitable for large-scale experiments while maintaining a high protein:lipid ratio. We demonstrate that incorporation of SecYEG into GUVs does not inhibit its translocation efficiency. Robust membrane protein functionalized proteo-GUVs are promising and flexible compartments for use in the formation and growth of synthetic cells.
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Affiliation(s)
- Ludo L J Schoenmakers
- Physical-Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Max J den Uijl
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jelle L Postma
- General Instrumentation, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Tim A P van den Akker
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Wilhelm T S Huck
- Physical-Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Arnold J M Driessen
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
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27
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Nazir A, Shad M, Rehman HM, Azim N, Sajjad M. Application of SUMO fusion technology for the enhancement of stability and activity of lysophospholipase from Pyrococcus abyssi. World J Microbiol Biotechnol 2024; 40:183. [PMID: 38722449 DOI: 10.1007/s11274-024-03998-w] [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: 02/11/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024]
Abstract
Heterologous production of proteins in Escherichia coli has raised several challenges including soluble production of target proteins, high levels of expression and purification. Fusion tags can serve as the important tools to overcome these challenges. SUMO (small ubiquitin-related modifier) is one of these tags whose fusion to native protein sequence can enhance its solubility and stability. In current research, a simple, efficient and cost-effective method is being discussed for the construction of pET28a-SUMO vector. In order to improve the stability and activity of lysophospholipase from Pyrococcus abyssi (Pa-LPL), a 6xHis-SUMO tag was fused to N-terminal of Pa-LPL by using pET28a-SUMO vector. Recombinant SUMO-fused enzyme (6 H-S-PaLPL) works optimally at 35 °C and pH 6.5 with remarkable thermostability at 35-95 °C. Thermo-inactivation kinetics of 6 H-S-PaLPL were also studied at 35-95 °C with first order rate constant (kIN) of 5.58 × 10- 2 h-1 and half-life of 12 ± 0 h at 95 °C. Km and Vmax for the hydrolysis of 4-nitrophenyl butyrate were calculated to be 2 ± 0.015 mM and 3882 ± 22.368 U/mg, respectively. 2.4-fold increase in Vmax of Pa-LPL was observed after fusion of 6xHis-SUMO tag to its N-terminal. It is the first report on the utilization of SUMO fusion tag to enhance the overall stability and activity of Pa-LPL. Fusion of 6xHis-SUMO tag not only aided in the purification process but also played a crucial role in increasing the thermostability and activity of the enzyme. SUMO-fused enzyme, thus generated, can serve as an important candidate for degumming of vegetable oils at industrial scale.
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Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mohsin Shad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Naseema Azim
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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28
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Johnson AO, Shipman BM, Hunt BC, Learman BS, Brauer AL, Zhou SP, Blair RH, De Nisco NJ, Armbruster CE. Function and contribution of two putative Enterococcus faecalis glycosaminoglycan degrading enzymes to bacteremia and catheter-associated urinary tract infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593205. [PMID: 38766094 PMCID: PMC11100720 DOI: 10.1101/2024.05.08.593205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Enterococcus faecalis is a common cause of healthcare acquired bloodstream infections and catheter associated urinary tract infections (CAUTI) in both adults and children. Treatment of E. faecalis infection is frequently complicated by multi-drug resistance. Based on protein homology, E. faecalis encodes two putative hyaluronidases, EF3023 (HylA) and EF0818 (HylB). In other Gram-positive pathogens, hyaluronidases have been shown to contribute to tissue damage and immune evasion, but function in E. faecalis has yet to be explored. Here, we show that both hylA and hylB contribute to E. faecalis pathogenesis. In a CAUTI model, Δ hylA exhibited defects in bladder colonization and dissemination to the bloodstream, and Δ hylB exhibited a defect in kidney colonization. Furthermore, a Δ hylA Δ hylB double mutant exhibited a severe colonization defect in a model of bacteremia while the single mutants colonized to a similar level as the wild-type strain, suggesting potential functional redundancy within the bloodstream. We next examined enzymatic activity, and demonstrate that HylB is capable of digesting both HA and CS in vitro while HylA exhibits only a very modest activity against heparin. Importantly, HA degradation by HylB provided a modest increase in cell density during stationary phase and also contributed to dampening of LPS-mediated NF-Bκ activation. Overall, these data demonstrate that glycosaminoglycan degradation is important for E. faecalis pathogenesis in the urinary tract and during bloodstream infection.
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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Muñoz-Muñoz PLA, Terán-Ramírez C, Mares-Alejandre RE, Márquez-González AB, Madero-Ayala PA, Meléndez-López SG, Ramos-Ibarra MA. Surface Engineering of Escherichia coli to Display Its Phytase (AppA) and Functional Analysis of Enzyme Activities. Curr Issues Mol Biol 2024; 46:3424-3437. [PMID: 38666945 PMCID: PMC11048855 DOI: 10.3390/cimb46040215] [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: 03/18/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Escherichia coli phytase (AppA) is widely used as an exogenous enzyme in monogastric animal feed mainly because of its ability to degrade phytic acid or its salt (phytate), a natural source of phosphorus. Currently, successful recombinant production of soluble AppA has been achieved by gene overexpression using both bacterial and yeast systems. However, some methods for the biomembrane immobilization of phytases (including AppA), such as surface display on yeast cells and bacterial spores, have been investigated to avoid expensive enzyme purification processes. This study explored a homologous protein production approach for displaying AppA on the cell surface of E. coli by engineering its outer membrane (OM) for extracellular expression. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of total bacterial lysates and immunofluorescence microscopy of non-permeabilized cells revealed protein expression, whereas activity assays using whole cells or OM fractions indicated functional enzyme display, as evidenced by consistent hydrolytic rates on typical substrates (i.e., p-nitrophenyl phosphate and phytic acid). Furthermore, the in vitro results obtained using a simple method to simulate the gastrointestinal tract of poultry suggest that the whole-cell biocatalyst has potential as a feed additive. Overall, our findings support the notion that biomembrane-immobilized enzymes are reliable for the hydrolysis of poorly digestible substrates relevant to animal nutrition.
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Affiliation(s)
- Patricia L. A. Muñoz-Muñoz
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
| | - Celina Terán-Ramírez
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
- Biochemical Sciences Graduate Program (Doctorate Studies), National Autonomous University of Mexico, Cuernavaca 62210, MOR, Mexico
| | - Rosa E. Mares-Alejandre
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
| | - Ariana B. Márquez-González
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
- Biological and Biomedical Sciences Graduate Program (Doctorate Studies), University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo A. Madero-Ayala
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
- Science and Engineering Graduate Program (Doctorate Studies), Autonomous University of Baja California, Tijuana 22390, BCN, Mexico
| | - Samuel G. Meléndez-López
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
| | - Marco A. Ramos-Ibarra
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
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da Costa Rodrigues T, Zorzete P, Miyaji EN, Gonçalves VM. Novel method for production and purification of untagged pneumococcal surface protein A from clade 1. Appl Microbiol Biotechnol 2024; 108:281. [PMID: 38570417 PMCID: PMC10990985 DOI: 10.1007/s00253-024-13098-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
Streptococcus pneumoniae can cause diseases with high mortality and morbidity. The licensed vaccines are based on capsular polysaccharides and induce antibodies with low cross reactivity, leading to restricted coverage of serotypes. For surpassing this limitation, new pneumococcal vaccines are needed for induction of broader protection. One important candidate is the pneumococcal surface protein A (PspA), which can be classified in 6 clades and 3 families. We have reported an efficient process for production and purification of untagged recombinant PspA from clade 4 (PspA4Pro). We now aim to obtain a highly pure recombinant PspA from clade 1 (PspA1) to be included, together with PspA4Pro, in a vaccine formulation to broaden response against pneumococci. The vector pET28a-pspA1 was constructed and used to transform Escherichia coli BL21(DE3) strain. One clone with high production of PspA1 was selected and adapted to high-density fermentation (HDF) medium. After biomass production in 6 L HDF using a bioreactor, the purification was defined after testing 3 protocols. During the batch bioreactor cultivation, plasmid stability remained above 90% and acetate formation was not detected. The final protein purification process included treatment with a cationic detergent after lysis, anion exchange chromatography, cryoprecipitation, cation exchange chromatography, and multimodal chromatography. The final purification process showed PspA1 purity of 93% with low endotoxin content and an overall recovery above 20%. The novel established process can be easily scaled-up and proved to be efficient to obtain a highly pure untagged PspA1 for inclusion in vaccine formulations. KEY POINTS: • Purification strategy for recombinant PspA1 from Streptococcus pneumoniae • Downstream processing for untagged protein antigens, the case of PspA1 • Purification strategy for PspA variants relies on buried amino acids in their sequences.
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Affiliation(s)
- Tasson da Costa Rodrigues
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades Em Biotecnologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Patricia Zorzete
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Eliane Namie Miyaji
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades Em Biotecnologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Viviane Maimoni Gonçalves
- Programa de Pós-Graduação Interunidades Em Biotecnologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, São Paulo, Brazil.
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Lara AR, Utrilla J, Martínez LM, Krausch N, Kaspersetz L, Hidalgo D, Cruz-Bournazou N, Neubauer P, Sigala JC, Gosset G, Büchs J. Recombinant protein expression in proteome-reduced cells under aerobic and oxygen-limited regimes. Biotechnol Bioeng 2024; 121:1216-1230. [PMID: 38178599 DOI: 10.1002/bit.28645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/18/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
Industrial cultures are hindered by the physiological complexity of the host and the limited mass transfer capacity of conventional bioreactors. In this study, a minimal cell approach was combined with genetic devices to overcome such issues. A flavin mononucleotide-based fluorescent protein (FbFP) was expressed in a proteome-reduced Escherichia coli (PR). When FbFP was expressed from a constitutive protein generator (CPG), the PR strain produced 47% and 35% more FbFP than its wild type (WT), in aerobic or oxygen-limited regimes, respectively. Metabolic and expression models predicted more efficient biomass formation at higher fluxes to FbFP, in agreement with these results. A microaerobic protein generator (MPG) and a microaerobic transcriptional cascade (MTC) were designed to induce FbFP expression upon oxygen depletion. The FbFP fluorescence using the MTC in the PR strain was 9% higher than that of the WT bearing the CPG under oxygen limitation. To further improve the PR strain, the pyruvate dehydrogenase complex regulator gene was deleted, and the Vitreoscilla hemoglobin was expressed. Compared to oxygen-limited cultures of the WT, the engineered strains increased the FbFP expression more than 50% using the MTC. Therefore, the designed expression systems can be a valuable alternative for industrial cultivations.
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Affiliation(s)
- Alvaro R Lara
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Jose Utrilla
- Synthetic Biology Program, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Luz María Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Niels Krausch
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Lucas Kaspersetz
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - David Hidalgo
- Synthetic Biology Program, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
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Hardebeck S, Jácobo Goebbels N, Michalski C, Schreiber S, Jose J. Identification of a potent PCNA-p15-interaction inhibitor by autodisplay-based peptide library screening. Microb Biotechnol 2024; 17:e14471. [PMID: 38646975 PMCID: PMC11033925 DOI: 10.1111/1751-7915.14471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/04/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is an essential factor for DNA metabolism. The influence of PCNA on DNA replication and repair, combined with the high expression rate of PCNA in various tumours renders PCNA a promising target for cancer therapy. In this context, an autodisplay-based screening method was developed to identify peptidic PCNA interaction inhibitors. A 12-mer randomized peptide library consisting of 2.54 × 106 colony-forming units was constructed and displayed at the surface of Escherichia coli BL21 (DE3) cells by autodisplay. Cells exhibiting an enhanced binding to fluorescent mScarlet-I-PCNA were enriched in four sorting rounds by flow cytometry. This led to the discovery of five peptide variants with affinity to mScarlet-I-PCNA. Among these, P3 (TCPLRWITHDHP) exhibited the highest binding signal. Subsequent flow cytometric analysis revealed a dissociation constant of 0.62 μM for PCNA-P3 interaction. Furthermore, the inhibition of PCNA interactions was investigated using p15, a PIP-box containing protein involved in DNA replication and repair. P3 inhibited the PCNA-p1551-70 interaction with a half maximal inhibitory activity of 16.2 μM, characterizing P3 as a potent inhibitor of the PCNA-p15 interaction.
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Affiliation(s)
- Sarah Hardebeck
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | | | - Caroline Michalski
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | - Sebastian Schreiber
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | - Joachim Jose
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
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Möller AM, Vázquez-Hernández M, Kutscher B, Brysch R, Brückner S, Marino EC, Kleetz J, Senges CHR, Schäkermann S, Bandow JE, Narberhaus F. Common and varied molecular responses of Escherichia coli to five different inhibitors of the lipopolysaccharide biosynthetic enzyme LpxC. J Biol Chem 2024; 300:107143. [PMID: 38458396 PMCID: PMC10998244 DOI: 10.1016/j.jbc.2024.107143] [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: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024] Open
Abstract
A promising yet clinically unexploited antibiotic target in difficult-to-treat Gram-negative bacteria is LpxC, the key enzyme in the biosynthesis of lipopolysaccharides, which are the major constituents of the outer membrane. Despite the development of dozens of chemically diverse LpxC inhibitor molecules, it is essentially unknown how bacteria counteract LpxC inhibition. Our study provides comprehensive insights into the response against five different LpxC inhibitors. All compounds bound to purified LpxC from Escherichia coli. Treatment of E. coli with these compounds changed the cell shape and stabilized LpxC suggesting that FtsH-mediated proteolysis of the inactivated enzyme is impaired. LpxC inhibition sensitized E. coli to vancomycin and rifampin, which poorly cross the outer membrane of intact cells. Four of the five compounds led to an accumulation of lyso-phosphatidylethanolamine, a cleavage product of phosphatidylethanolamine, generated by the phospholipase PldA. The combined results suggested an imbalance in lipopolysaccharides and phospholipid biosynthesis, which was corroborated by the global proteome response to treatment with the LpxC inhibitors. Apart from LpxC itself, FabA and FabB responsible for the biosynthesis of unsaturated fatty acids were consistently induced. Upregulated compound-specific proteins are involved in various functional categories, such as stress reactions, nucleotide, or amino acid metabolism and quorum sensing. Our work shows that antibiotics targeting the same enzyme do not necessarily elicit identical cellular responses. Moreover, we find that the response of E. coli to LpxC inhibition is distinct from the previously reported response in Pseudomonas aeruginosa.
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Affiliation(s)
- Anna-Maria Möller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Blanka Kutscher
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Raffael Brysch
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Simon Brückner
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Emily C Marino
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia Kleetz
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Christoph H R Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
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Bull JJ, Wichman HA, Krone SM, Molineux IJ. Controlling Recombination to Evolve Bacteriophages. Cells 2024; 13:585. [PMID: 38607024 PMCID: PMC11011186 DOI: 10.3390/cells13070585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/07/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Recombination among different phages sometimes facilitates their ability to grow on new hosts. Protocols to direct the evolution of phage host range, as might be used in the application of phage therapy, would then benefit from including steps to enable recombination. Applying mathematical and computational models, in addition to experiments using phages T3 and T7, we consider ways that a protocol may influence recombination levels. We first address coinfection, which is the first step to enabling recombination. The multiplicity of infection (MOI, the ratio of phage to cell concentration) is insufficient for predicting (co)infection levels. The force of infection (the rate at which cells are infected) is also critical but is more challenging to measure. Using both a high force of infection and high MOI (>1) for the different phages ensures high levels of coinfection. We also apply a four-genetic-locus model to study protocol effects on recombinant levels. Recombinants accumulate over multiple generations of phage growth, less so if one phage outgrows the other. Supplementing the phage pool with the low-fitness phage recovers some of this 'lost' recombination. Overall, fine tuning of phage recombination rates will not be practical with wild phages, but qualitative enhancement can be attained with some basic procedures.
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Affiliation(s)
- James J. Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA;
| | - Holly A. Wichman
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA;
| | - Stephen M. Krone
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA;
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID 83844, USA
| | - Ian J. Molineux
- Institute for Cell and Molecular Biology, Department of Molecular Biosciences, LaMontagne Center for Infectious Diseases, The University of Texas, Austin, TX 78712, USA;
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Ensinck D, Gerhardt ECM, Rollan L, Huergo LF, Gramajo H, Diacovich L. The PII protein interacts with the Amt ammonium transport and modulates nitrate/nitrite assimilation in mycobacteria. Front Microbiol 2024; 15:1366111. [PMID: 38591044 PMCID: PMC11001197 DOI: 10.3389/fmicb.2024.1366111] [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: 01/05/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
PII proteins are signal transduction proteins that belong to a widely distributed family of proteins involved in the modulation of different metabolisms in bacteria. These proteins are homotrimers carrying a flexible loop, named T-loop, which changes its conformation due to the recognition of diverse key metabolites, ADP, ATP, and 2-oxoglutarate. PII proteins interact with different partners to primarily regulate a set of nitrogen pathways. In some organisms, PII proteins can also control carbon metabolism by interacting with the biotin carboxyl carrier protein (BCCP), a key component of the acetyl-CoA carboxylase (ACC) enzyme complex, inhibiting its activity with the consequent reduction of fatty acid biosynthesis. Most bacteria contain at least two PII proteins, named GlnB and GlnK, with different regulatory roles. In mycobacteria, only one PII protein was identified, and the three-dimensional structure was solved, however, its physiological role is unknown. In this study we purified the Mycobacterium tuberculosis (M. tb) PII protein, named GlnB, and showed that it weakly interacts with the AccA3 protein, the α subunit shared by the three different, and essential, Acyl-CoA carboxylase complexes (ACCase 4, 5, and 6) present in M. tb. A M. smegmatis deletion mutant, ∆MsPII, exhibited a growth deficiency on nitrate and nitrite as unique nitrogen sources, and accumulated nitrite in the culture supernatant. In addition, M. tb PII protein was able to interact with the C-terminal domain of the ammonium transporter Amt establishing the ancestral role for this PII protein as a GlnK functioning protein.
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Affiliation(s)
- Delfina Ensinck
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Edileusa C. M. Gerhardt
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Lara Rollan
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano F. Huergo
- Setor Litoral, Federal University of Paraná, Universidade Federal do Paraná (UFPR), Matinhos, Paraná, Brazil
- Graduated Program in Sciences-Biochemistry, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Hugo Gramajo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Tao K, Narita SI, Okada U, Murakami S, Tokuda H. Dissection of an ABC transporter LolCDE function analyzed by photo-crosslinking. J Biochem 2024; 175:427-437. [PMID: 38156779 PMCID: PMC11005994 DOI: 10.1093/jb/mvad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024] Open
Abstract
The envelope of Escherichia coli contains approximately 100 different species of lipoproteins, most of which are localized to the inner leaflet of the outer membrane. The localization of lipoprotein (Lol) system, consisting of five Lol proteins, is responsible for the trafficking of lipoproteins to the outer membrane. LolCDE binds to lipoproteins destined for the outer membrane and transfers them to the periplasmic chaperone LolA. Although the cryo-EM structures of E. coli LolCDE have been reported, the mechanisms by which outer membrane lipoproteins are transferred to LolA remain elusive. In this study, we investigated the interaction between LolCDE and lipoproteins using site-specific photo-crosslinking. We introduced a photo-crosslinkable amino acid into different locations across the four helices which form the central lipoprotein-binding cavity, and identified domains that crosslink with peptidoglycan-associated lipoprotein (Pal) in vivo. Using one of the derivatives containing the photo-crosslinkable amino acid, we developed an in vitro system to analyze the binding of lipoproteins to LolCDE. Our results indicate that compound 2, a LolCDE inhibitor, does not inhibit the binding of lipoproteins to LolCDE, but rather promotes the dissociation of bound lipoproteins from LolCDE.
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Affiliation(s)
- Kazuyuki Tao
- Isotope Science Center, University of Tokyo, 2-11-16 Yayoi, Bunky-ku, Tokyo 113-0032, Japan
| | - Shin-ichiro Narita
- Faculty of Health and Nutrition, Yamagata Prefectural Yonezawa University of Nutrition Sciences, Yonezawa, Yamagata 992-0025, Japan
| | - Ui Okada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Hajime Tokuda
- Faculty of Nutritional Sciences, University of Morioka, Takizawa, Iwate 020-0694, Japan
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Wenzel S, Hess R, Kiefer D, Kuhn A. Involvement of the Cell Division Protein DamX in the Infection Process of Bacteriophage T4. Viruses 2024; 16:487. [PMID: 38675830 PMCID: PMC11054660 DOI: 10.3390/v16040487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
The molecular mechanism of how the infecting DNA of bacteriophage T4 passes from the capsid through the bacterial cell wall and enters the cytoplasm is essentially unknown. After adsorption, the short tail fibers of the infecting phage extend from the baseplate and trigger the contraction of the tail sheath, leading to a puncturing of the outer membrane by the tail tip needle composed of the proteins gp5.4, gp5 and gp27. To explore the events that occur in the periplasm and at the inner membrane, we constructed T4 phages that have a modified gp27 in their tail tip with a His-tag. Shortly after infection with these phages, cells were chemically cross-linked and solubilized. The cross-linked products were affinity-purified on a nickel column and the co-purified proteins were identified by mass spectrometry, and we found that predominantly the inner membrane proteins DamX, SdhA and PpiD were cross-linked. The same partner proteins were identified when purified gp27 was added to Escherichia coli spheroplasts, suggesting a direct protein-protein interaction.
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Affiliation(s)
| | | | | | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, 190h, Garbenstr. 30, 70599 Stuttgart, Germany; (S.W.); (R.H.); (D.K.)
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Hansen AL, Theisen FF, Crehuet R, Marcos E, Aghajari N, Willemoës M. Carving out a Glycoside Hydrolase Active Site for Incorporation into a New Protein Scaffold Using Deep Network Hallucination. ACS Synth Biol 2024; 13:862-875. [PMID: 38357862 PMCID: PMC10949244 DOI: 10.1021/acssynbio.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Enzymes are indispensable biocatalysts for numerous industrial applications, yet stability, selectivity, and restricted substrate recognition present limitations for their use. Despite the importance of enzyme engineering in overcoming these limitations, success is often challenged by the intricate architecture of enzymes derived from natural sources. Recent advances in computational methods have enabled the de novo design of simplified scaffolds with specific functional sites. Such scaffolds may be advantageous as platforms for enzyme engineering. Here, we present a strategy for the de novo design of a simplified scaffold of an endo-α-N-acetylgalactosaminidase active site, a glycoside hydrolase from the GH101 enzyme family. Using a combination of trRosetta hallucination, iterative cycles of deep-learning-based structure prediction, and ProteinMPNN sequence design, we designed proteins with 290 amino acids incorporating the active site while reducing the molecular weight by over 100 kDa compared to the initial endo-α-N-acetylgalactosaminidase. Of 11 tested designs, six were expressed as soluble monomers, displaying similar or increased thermostabilities compared to the natural enzyme. Despite lacking detectable enzymatic activity, the experimentally determined crystal structures of a representative design closely matched the design with a root-mean-square deviation of 1.0 Å, with most catalytically important side chains within 2.0 Å. The results highlight the potential of scaffold hallucination in designing proteins that may serve as a foundation for subsequent enzyme engineering.
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Affiliation(s)
- Anders Lønstrup Hansen
- The
Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular
Sciences, Department of Biology, University
of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Frederik Friis Theisen
- The
Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular
Sciences, Department of Biology, University
of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Ramon Crehuet
- Institute
for Advanced Chemistry of Catalonia (IQAC), CSIC, Carrer Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Enrique Marcos
- Protein
Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), CSIC, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Nushin Aghajari
- Molecular
Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, F-69367 Lyon CEDEX 07, France
| | - Martin Willemoës
- The
Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular
Sciences, Department of Biology, University
of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
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Zhang Y, Anbir S, McTiernan J, Li S, Worcester M, Mishra P, Colvin ME, Gopinathan A, Mohideen U, Zandi R, Kuhlman TE. Synthesis, insertion, and characterization of SARS-CoV-2 membrane protein within lipid bilayers. SCIENCE ADVANCES 2024; 10:eadm7030. [PMID: 38416838 PMCID: PMC10901468 DOI: 10.1126/sciadv.adm7030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Throughout history, coronaviruses have posed challenges to both public health and the global economy; nevertheless, methods to combat them remain rudimentary, primarily due to the absence of experiments to understand the function of various viral components. Among these, membrane (M) proteins are one of the most elusive because of their small size and challenges with expression. Here, we report the development of an expression system to produce tens to hundreds of milligrams of M protein per liter of Escherichia coli culture. These large yields render many previously inaccessible structural and biophysical experiments feasible. Using cryo-electron microscopy and atomic force microscopy, we image and characterize individual membrane-incorporated M protein dimers and discover membrane thinning in the vicinity, which we validated with molecular dynamics simulations. Our results suggest that the resulting line tension, along with predicted induction of local membrane curvature, could ultimately drive viral assembly and budding.
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Affiliation(s)
- Yuanzhong Zhang
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
| | - Sara Anbir
- Biophysics Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Joseph McTiernan
- Department of Physics, University of California, Merced, Merced, CA 95340, USA
| | - Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
| | - Michael Worcester
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
| | - Pratyasha Mishra
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Michael E. Colvin
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA 95340, USA
| | - Ajay Gopinathan
- Department of Physics, University of California, Merced, Merced, CA 95340, USA
| | - Umar Mohideen
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
- Biophysics Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
- Biophysics Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Thomas E. Kuhlman
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
- Biophysics Program, University of California, Riverside, Riverside, CA 92521, USA
- Microbiology Program, University of California, Riverside, Riverside, CA 92521, USA
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41
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Gercke D, Lenz F, Jose J. Split-GFP complementation at the bacterial cell surface for antibody-free labeling and quantification of heterologous protein display. Enzyme Microb Technol 2024; 174:110391. [PMID: 38176324 DOI: 10.1016/j.enzmictec.2023.110391] [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: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
The split-GFP system is a versatile tool with numerous applications, but it has been underutilized for the labeling of heterologous surface-displayed proteins. By inserting the 16 amino acid sequence of the GFP11-tag between a protein of interest and an autotransporter protein, it is possible to present a protein at the outer membrane of gram-negative bacteria and to fluorescently label it by complementation with externally added GFP1-10. The labeled cells could be clearly discerned from cells without the protein of interest using flow cytometry and the insertion of the GFP11-tag caused no significant alteration of the catalytic activity for the tested model enzyme CsBglA. Furthermore, the amount of the protein of interest on the cells could be quantified by comparing the green fluorescence resulting from the complementation to that of standards with known concentrations. This allows a precise characterization of whole-cell biocatalysts, which is difficult with existing methods. The split-GFP complementation approach was shown to be specific, in a similar manner as commercial antibodies. It is cost-efficient, minimizes the possibility of adverse effects on protein expression or solubility, and can be performed at high throughput.
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Affiliation(s)
- David Gercke
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany
| | - Florian Lenz
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany
| | - Joachim Jose
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany.
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42
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Després PC, Dubé AK, Grenier J, Picard MÈ, Shi R, Landry CR. Compensatory mutations potentiate constructive neutral evolution by gene duplication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579783. [PMID: 38405844 PMCID: PMC10888846 DOI: 10.1101/2024.02.12.579783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Protein functions generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicate and evolve an homodimeric enzyme to examine if and how this could happen. We identify hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when co-expressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate.
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Affiliation(s)
- Philippe C Després
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
| | - Alexandre K Dubé
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
| | - Jordan Grenier
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Rong Shi
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
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Nie M, Wang J, Zhang K. Engineering a Novel Acetyl-CoA Pathway for Efficient Biosynthesis of Acetyl-CoA-Derived Compounds. ACS Synth Biol 2024; 13:358-369. [PMID: 38151239 DOI: 10.1021/acssynbio.3c00613] [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: 12/29/2023]
Abstract
Acetyl-CoA is an essential central metabolite in living organisms and a key precursor for various value-added products as well. However, the intracellular availability of acetyl-CoA limits the efficient production of these target products due to complex and strict regulation. Here, we proposed a new acetyl-CoA pathway, relying on two enzymes, threonine aldolase and acetaldehyde dehydrogenase (acetylating), which can convert one l-threonine into one acetyl-CoA, one glycine, and generate one NADH, without carbon loss. Introducing the acetyl-CoA pathway could increase the intracellular concentration of acetyl-CoA by 8.6-fold compared with the wild-type strain. To develop a cost-competitive and genetically stable acetyl-CoA platform strain, the new acetyl-CoA pathway, driven by the constitutive strong promoter, was integrated into the chromosome of Escherichia coli. We demonstrated the practical application of this new acetyl-CoA pathway by high titer production of β-alanine, mevalonate, and N-acetylglucosamine. At the same time, this pathway achieved a high-yield production of glycine, a value-added commodity chemical for the synthesis of glyphosate and thiamphenicol. This work shows the potential of this new acetyl-CoA pathway for the industrial production of acetyl-CoA-derived compounds.
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Affiliation(s)
- Mengzhen Nie
- Zhejiang University, Hangzhou, Zhejiang 310027, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Jingyu Wang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Kechun Zhang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
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Hussain A, Ray MK. Role of DEAD-box RNA helicases in low-temperature adapted growth of Antarctic Pseudomonas syringae Lz4W. Microbiol Spectr 2024; 12:e0433522. [PMID: 38014988 PMCID: PMC10783127 DOI: 10.1128/spectrum.04335-22] [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: 11/06/2022] [Accepted: 10/16/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE RNA metabolism is important as RNA acts as a link between genomic information and functional biomolecules, thereby playing a critical role in cellular response to environment. We investigated the role of DEAD-box RNA helicases in low-temperature adapted growth of P. syringae, as this group of enzymes play an essential role in modulation of RNA secondary structures. This is the first report on the assessment of all major DEAD-box RNA helicases in any Antarctic bacterium. Of the five RNA helicases, three (srmB, csdA, and dbpA) are important for the growth of the Antarctic P. syringae at low temperature. However, the requisite role of dbpA and the indispensable requirement of csdA for low-temperature adapted growth are a novel finding of this study. Growth analysis of combinatorial deletion strains was performed to understand the functional interaction among helicase genes. Similarly, genetic complementation of RNA helicase mutants was conducted for identification of gene redundancy in P. syringae.
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Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Malay Kumar Ray
- Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
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45
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Mokhtari S, Saris PEJ, Takala TM. Heterologous expression and purification of the phage lysin-like bacteriocin LysL from Lactococcus lactis LAC460. FEMS Microbiol Lett 2024; 371:fnae065. [PMID: 39153967 PMCID: PMC11370637 DOI: 10.1093/femsle/fnae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/12/2024] [Accepted: 08/16/2024] [Indexed: 08/19/2024] Open
Abstract
The wild-type Lactococcus lactis strain LAC460 produces two bacteriocin-like phage lysins, LysL and LysP. This study aimed to produce and secrete LysL in various heterologous hosts and an in vitro cell-free expression system for further functional studies. Initially, the lysL gene from L. lactis LAC460 was cloned into Lactococcus cremoris NZ9000 and L. lactis N8 strains, with and without the usp45 signal sequence (SSusp45), under a nisin-inducible promoter. Active LysL was primarily produced intracellularly in recombinant L. lactis N8, with some secretion into the supernatant. Recombinant L. cremoris NZ9000 lysed upon nisin induction, indicating successful lysL expression. However, fusion with Usp45 signal peptide (SPUsp45-LysL) weakened LysL activity, likely due to incomplete signal peptide cleavage during secretion. Active LysL was also produced in vitro, and analysed in SDS-PAGE, giving a 42-kDa band. However, the yield of LysL protein was still low when produced from recombinant lactococci or by in vitro expression system. Therefore, His-tagged LysL was produced in Escherichia coli BL21(DE3). Western blot confirmed the intracellular production of about 44-kDa His-tagged LysL in E. coli. His-tagged active LysL was then purified by Ni-NTA affinity chromatography yielding sufficient 4.34 mg of protein to be used in future functional studies.
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Affiliation(s)
- Samira Mokhtari
- Department of Microbiology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
| | - Per E J Saris
- Department of Microbiology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
| | - Timo M Takala
- Department of Microbiology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
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46
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Vazulka S, Schiavinato M, Tauer C, Wagenknecht M, Cserjan-Puschmann M, Striedner G. RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling. Microb Cell Fact 2024; 23:14. [PMID: 38183013 PMCID: PMC10768439 DOI: 10.1186/s12934-023-02278-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Escherichia coli is a cost-effective expression system for production of antibody fragments like Fabs. Various yield improvement strategies have been applied, however, Fabs remain challenging to produce. This study aimed to characterize the gene expression response of commonly used E. coli strains BL21(DE3) and HMS174(DE3) to periplasmic Fab expression using RNA sequencing (RNA-seq). Two Fabs, Fabx and FTN2, fused to a post-translational translocation signal sequence, were produced in carbon-limited fed-batch cultivations. RESULTS Production of Fabx impeded cell growth substantially stronger than FTN2 and yields of both Fabs differed considerably. The most noticeable, common changes in Fab-producing cells suggested by our RNA-seq data concern the cell envelope. The Cpx and Psp stress responses, both connected to inner membrane integrity, were activated, presumably by recombinant protein aggregation and impairment of the Sec translocon. The data additionally suggest changes in lipopolysaccharide synthesis, adjustment of membrane permeability, and peptidoglycan maturation and remodeling. Moreover, all Fab-producing strains showed depletion of Mg2+, indicated by activation of the PhoQP two-component signal transduction system during the early stage and sulfur and phosphate starvation during the later stage of the process. Furthermore, our data revealed ribosome stalling, caused by the Fabx amino acid sequence, as a contributor to low Fabx yields. Increased Fabx yields were obtained by a site-specific amino acid exchange replacing the stalling sequence. Contrary to expectations, cell growth was not impacted by presence or removal of the stalling sequence. Considering ribosome rescue is a conserved mechanism, the substantial differences observed in gene expression between BL21(DE3) and HMS174(DE3) in response to ribosome stalling on the recombinant mRNA were surprising. CONCLUSIONS Through characterization of the gene expression response to Fab production under industrially relevant cultivation conditions, we identified potential cell engineering targets. Thereby, we hope to enable rational approaches to improve cell fitness and Fab yields. Furthermore, we highlight ribosome stalling caused by the amino acid sequence of the recombinant protein as a possible challenge during recombinant protein production.
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Affiliation(s)
- Sophie Vazulka
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV, GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1120, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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47
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den Uijl MJ, Driessen AJM. Phospholipid dependency of membrane protein insertion by the Sec translocon. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184232. [PMID: 37734458 DOI: 10.1016/j.bbamem.2023.184232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023]
Abstract
Membrane protein insertion into and translocation across the bacterial cytoplasmic membrane are essential processes facilitated by the Sec translocon. Membrane insertion occurs co-translationally whereby the ribosome nascent chain is targeted to the translocon via signal recognition particle and its receptor FtsY. The phospholipid dependence of membrane protein insertion has remained mostly unknown. Here we assessed in vitro the dependence of the SecA independent insertion of the mannitol permease MtlA into the membrane on the main phospholipid species present in Escherichia coli. We observed that insertion depends on the presence of phosphatidylglycerol and is due to the anionic nature of the polar headgroup, while insertion is stimulated by the zwitterionic phosphatidylethanolamine. We found an optimal insertion efficiency at about 30 mol% DOPG and 50 mol% DOPE which approaches the bulk membrane phospholipid composition of E. coli.
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Affiliation(s)
- Max J den Uijl
- University of Groningen, Groningen Biomolecular Sciences and Biotechnology, 9747 AG Groningen, the Netherlands
| | - Arnold J M Driessen
- University of Groningen, Groningen Biomolecular Sciences and Biotechnology, 9747 AG Groningen, the Netherlands.
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48
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Kumar A, Kamuju V, Vivekanandan P. RNA G-quadruplexes inhibit translation of the PE/PPE transcripts in Mycobacterium tuberculosis. J Biol Chem 2024; 300:105567. [PMID: 38103641 PMCID: PMC10801317 DOI: 10.1016/j.jbc.2023.105567] [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: 08/21/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023] Open
Abstract
The role of RNA G-quadruplexes (rG4s) in bacteria remains poorly understood. High G-quadruplex densities have been linked to organismal stress. Here we investigate rG4s in mycobacteria, which survive highly stressful conditions within the host. We show that rG4-enrichment is a unique feature exclusive to slow-growing pathogenic mycobacteria, and Mycobacterium tuberculosis (Mtb) transcripts contain an abundance of folded rG4s. Notably, the PE/PPE family of genes, unique to slow-growing pathogenic mycobacteria, contain over 50% of rG4s within Mtb transcripts. We found that RNA oligonucleotides of putative rG4s in PE/PPE genes form G-quadruplex structures in vitro, which are stabilized by the G-quadruplex ligand BRACO19. Furthermore, BRACO19 inhibits the transcription of PE/PPE genes and selectively suppresses the growth of Mtb but not Mycobacterium smegmatis or other rapidly growing bacteria. Importantly, the stabilization of rG4s inhibits the translation of Mtb PE/PPE genes (PPE56, PPE67, PPE68, PE_PGRS39, and PE_PGRS41) ectopically expressed in M. smegmatis or Escherichia coli. In addition, the rG4-mediated reduction in PE/PPE protein levels attenuates proinflammatory response upon infection of THP-1 cells. Our findings shed new light on the regulation of PE/PPE genes and highlight a pivotal role for rG4s in Mtb transcripts as regulators of post-transcriptional translational control. The rG4s in mycobacterial transcripts may represent potential drug targets for newer therapies.
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Affiliation(s)
- Ashish Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Vinay Kamuju
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India.
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Jiménez-Guerrero I, Sonawane M, Eckshtain-Levi N, Tuang ZK, da Silva GM, Pérez-Montaño F, Leibman-Markus M, Gupta R, Noda-Garcia L, Bar M, Burdman S. Natural variation in a short region of the Acidovorax citrulli type III-secreted effector AopW1 is associated with differences in cytotoxicity and host adaptation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:516-540. [PMID: 37864805 DOI: 10.1111/tpj.16507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
Bacterial fruit blotch, caused by Acidovorax citrulli, is a serious disease of melon and watermelon. The strains of the pathogen belong to two major genetic groups: group I strains are strongly associated with melon, while group II strains are more aggressive on watermelon. A. citrulli secretes many protein effectors to the host cell via the type III secretion system. Here we characterized AopW1, an effector that shares similarity to the actin cytoskeleton-disrupting effector HopW1 of Pseudomonas syringae and with effectors from other plant-pathogenic bacterial species. AopW1 has a highly variable region (HVR) within amino acid positions 147 to 192, showing 14 amino acid differences between group I and II variants. We show that group I AopW1 is more toxic to yeast and Nicotiana benthamiana cells than group II AopW1, having stronger actin filament disruption activity, and increased ability to induce cell death and reduce callose deposition. We further demonstrated the importance of some amino acid positions within the HVR for AopW1 cytotoxicity. Cellular analyses revealed that AopW1 also localizes to the endoplasmic reticulum, chloroplasts, and plant endosomes. We also show that overexpression of the endosome-associated protein EHD1 attenuates AopW1-induced cell death and increases defense responses. Finally, we show that sequence variation in AopW1 plays a significant role in the adaptation of group I and II strains to their preferred hosts, melon and watermelon, respectively. This study provides new insights into the HopW1 family of bacterial effectors and provides first evidence on the involvement of EHD1 in response to biotic stress.
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Affiliation(s)
- Irene Jiménez-Guerrero
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Monica Sonawane
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noam Eckshtain-Levi
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Za Khai Tuang
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Gustavo Mateus da Silva
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Francisco Pérez-Montaño
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
- Department of Microbiology, University of Seville, Seville, Spain
| | - Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Institute, Bet Dagan, Israel
| | - Rupali Gupta
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Institute, Bet Dagan, Israel
| | - Lianet Noda-Garcia
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Institute, Bet Dagan, Israel
| | - Saul Burdman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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Jossier M, Oury C, Glab N, Hodges M. Purification of Recombinant N-terminal Histidine-Tagged Arabidopsis thaliana Phosphoglycolate Phosphatase 1, Glycolate Oxidase 1 and 2, and Hydroxypyruvate Reductase 1. Methods Mol Biol 2024; 2792:97-111. [PMID: 38861081 DOI: 10.1007/978-1-0716-3802-6_8] [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: 06/12/2024]
Abstract
To measure the kinetic properties of photorespiratory enzymes, it is necessary to work with purified proteins. Protocols to purify photorespiratory enzymes from leaves of various plant species require several time-consuming steps. It is now possible to produce large quantities of recombinant proteins in bacterial cells. They can be rapidly purified as histidine-tagged recombinant proteins by immobilized metal affinity chromatography using Ni2+-NTA-agarose. This chapter describes protocols to purify several Arabidopsis thaliana His-tagged recombinant photorespiratory enzymes (phosphoglycolate phosphatase, glycolate oxidase, and hydroxypyruvate reductase) from Escherichia coli cell cultures using two bacterial strain-plasmid systems: BL21(DE3)-pET and LMG194-pBAD.
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Affiliation(s)
- Mathieu Jossier
- Université Paris-Saclay, CNRS, INRAe, Université Paris Cité, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France.
| | - Céline Oury
- Université Paris-Saclay, CNRS, INRAe, Université Paris Cité, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Nathalie Glab
- Université Paris-Saclay, CNRS, INRAe, Université Paris Cité, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Michael Hodges
- Université Paris-Saclay, CNRS, INRAe, Université Paris Cité, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France.
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