51
|
Botero S, Chiaroni-Clarke R, Simon SM. Escherichia coli as a platform for the study of phosphoinositide biology. SCIENCE ADVANCES 2019; 5:eaat4872. [PMID: 30944849 PMCID: PMC6436935 DOI: 10.1126/sciadv.aat4872] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
Despite being a minor component of cells, phosphoinositides are essential for eukaryotic membrane biology, serving as markers of organelle identity and involved in several signaling cascades. Their many functions, combined with alternative synthesis pathways, make in vivo study very difficult. In vitro studies are limited by their inability to fully recapitulate the complexities of membranes in living cells. We engineered the biosynthetic pathway for the most abundant phosphoinositides into the bacterium Escherichia coli, which is naturally devoid of this class of phospholipids. These modified E. coli, when grown in the presence of myo-inositol, incorporate phosphatidylinositol (PI), phosphatidylinositol-4-phosphate (PI4P), phosphatidylinositol-4,5-bisphosphate (PIP2), and phosphatidylinositol-3,4,5-trisphosphate (PIP3) into their plasma membrane. We tested models of biophysical mechanisms with these phosphoinositides in a living membrane, using our system to evaluate the role of PIP2 in nonconventional protein export of human basic fibroblast growth factor 2. We found that PI alone is sufficient for the process.
Collapse
|
52
|
Amroudie MN, Ataei F. Experimental and theoretical study of IBC domain from human IP3R2; molecular cloning, bacterial expression and protein purification. Int J Biol Macromol 2019; 124:1321-1327. [DOI: 10.1016/j.ijbiomac.2018.09.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 12/01/2022]
|
53
|
A step forward: Compatible and dual-inducible expression vectors for gene co-expression in Corynebacterium glutamicum. Plasmid 2019; 101:20-27. [DOI: 10.1016/j.plasmid.2018.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/10/2018] [Accepted: 12/26/2018] [Indexed: 12/19/2022]
|
54
|
Chase J, Catalano A, Noble AJ, Eng ET, Olinares PD, Molloy K, Pakotiprapha D, Samuels M, Chait B, des Georges A, Jeruzalmi D. Mechanisms of opening and closing of the bacterial replicative helicase. eLife 2018; 7:41140. [PMID: 30582519 PMCID: PMC6391071 DOI: 10.7554/elife.41140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
Collapse
Affiliation(s)
- Jillian Chase
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States
| | - Andrew Catalano
- Department of Chemistry and Biochemistry, City College of New York, New York, United States
| | - Alex J Noble
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Edward T Eng
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Paul Db Olinares
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Kelly Molloy
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Danaya Pakotiprapha
- Department of Biochemistry, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Martin Samuels
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Brian Chait
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Amedee des Georges
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, United States
| |
Collapse
|
55
|
Hong YG, Moon YM, Hong JW, No SY, Choi TR, Jung HR, Yang SY, Bhatia SK, Ahn JO, Park KM, Yang YH. Production of glutaric acid from 5-aminovaleric acid using Escherichia coli whole cell bio-catalyst overexpressing GabTD from Bacillus subtilis. Enzyme Microb Technol 2018; 118:57-65. [DOI: 10.1016/j.enzmictec.2018.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/24/2018] [Accepted: 07/09/2018] [Indexed: 01/16/2023]
|
56
|
Schleicher L, Muras V, Claussen B, Pfannstiel J, Blombach B, Dibrov P, Fritz G, Steuber J. Vibrio natriegens as Host for Expression of Multisubunit Membrane Protein Complexes. Front Microbiol 2018; 9:2537. [PMID: 30410475 PMCID: PMC6209661 DOI: 10.3389/fmicb.2018.02537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is a convenient host for the expression of proteins, but the heterologous production of large membrane protein complexes often is hampered by the lack of specific accessory genes required for membrane insertion or cofactor assembly. In this study we introduce the non-pathogenic and fast-growing Vibrio natriegens as a suitable expression host for membrane-bound proteins from Vibrio cholerae. We achieved production of the primary Na+ pump, the NADH:quinone oxidoreductase (NQR), from V. cholerae in an active state, as indicated by increased overall NADH:quinone oxidoreduction activity of membranes from the transformed V. natriegens, and the sensitivity toward Ag+, a specific inhibitor of the NQR. Complete assembly of V. cholerae NQR expressed in V. natriegens was demonstrated by BN PAGE followed by activity staining. The secondary transport system Mrp from V. cholerae, another membrane-bound multisubunit complex, was also produced in V. natriegens in a functional state, as demonstrated by in vivo Li+ transport. V. natriegens is a promising expression host for the production of membrane protein complexes from Gram-negative pathogens.
Collapse
Affiliation(s)
- Lena Schleicher
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Valentin Muras
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Björn Claussen
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Mass Spectrometry Core Facility, University of Hohenheim, Stuttgart, Germany
| | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Pavel Dibrov
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Günter Fritz
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany.,Institute for Neuropathology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
57
|
Mesa-Pereira B, Rea MC, Cotter PD, Hill C, Ross RP. Heterologous Expression of Biopreservative Bacteriocins With a View to Low Cost Production. Front Microbiol 2018; 9:1654. [PMID: 30093889 PMCID: PMC6070625 DOI: 10.3389/fmicb.2018.01654] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/02/2018] [Indexed: 02/04/2023] Open
Abstract
Bacteriocins, a heterogenous group of antibacterial ribosomally synthesized peptides, have potential as bio-preservatives in in a wide range of foods and as future therapeutics for the inhibition of antibiotic-resistant bacteria. While many bacteriocins have been characterized, several factors limit their production in large quantities, a requirement to make them commercially viable for food or pharma applications. The identification of new bacteriocins by database mining has been promising, but their potential is difficult to evaluate in the absence of suitable expression systems. E. coli has been used as a heterologous host to produce recombinant proteins for decades and has an extensive set of expression vectors and strains available. Here, we review the different expression systems for bacteriocin production using this host and identify the most important features to guarantee successful production of a range of bacteriocins.
Collapse
Affiliation(s)
- Beatriz Mesa-Pereira
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mary C Rea
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,College of Science Engineering and Food Science, University College Cork, Cork, Ireland
| |
Collapse
|
58
|
Kenney GE, Dassama LMK, Pandelia ME, Gizzi AS, Martinie RJ, Gao P, DeHart CJ, Schachner LF, Skinner OS, Ro SY, Zhu X, Sadek M, Thomas PM, Almo SC, Bollinger JM, Krebs C, Kelleher NL, Rosenzweig AC. The biosynthesis of methanobactin. Science 2018; 359:1411-1416. [PMID: 29567715 DOI: 10.1126/science.aap9437] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/07/2018] [Indexed: 11/02/2022]
Abstract
Metal homeostasis poses a major challenge to microbes, which must acquire scarce elements for core metabolic processes. Methanobactin, an extensively modified copper-chelating peptide, was one of the earliest natural products shown to enable microbial acquisition of a metal other than iron. We describe the core biosynthetic machinery responsible for the characteristic posttranslational modifications that grant methanobactin its specificity and affinity for copper. A heterodimer comprising MbnB, a DUF692 family iron enzyme, and MbnC, a protein from a previously unknown family, performs a dioxygen-dependent four-electron oxidation of the precursor peptide (MbnA) to install an oxazolone and an adjacent thioamide, the characteristic methanobactin bidentate copper ligands. MbnB and MbnC homologs are encoded together and separately in many bacterial genomes, suggesting functions beyond their roles in methanobactin biosynthesis.
Collapse
Affiliation(s)
- Grace E Kenney
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Laura M K Dassama
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | | | - Anthony S Gizzi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ryan J Martinie
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peng Gao
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Caroline J DeHart
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Luis F Schachner
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Owen S Skinner
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Soo Y Ro
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Xiao Zhu
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Monica Sadek
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neil L Kelleher
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C Rosenzweig
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| |
Collapse
|
59
|
Liu J, Jiang J, Bai Y, Fan TP, Zhao Y, Zheng X, Cai Y. Mimicking a New 2-Phenylethanol Production Pathway from Proteus mirabilis JN458 in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3498-3504. [PMID: 29560727 DOI: 10.1021/acs.jafc.8b00627] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Bacteria rarely produce natural 2-phenylethanol. We verified a new pathway from Proteus mirabilis JN458 to produce 2-phenylethanol using Escherichia coli to coexpress l-amino acid deaminase, α-keto acid decarboxylase, and alcohol dehydrogenase from P. mirabilis. Based on this pathway, a glucose dehydrogenase coenzyme regeneration system was constructed. The optimal conditions of biotransformation by the recombinant strain E-pAEAKaG were at 40 °C and pH 7.0. Finally, the recombinant strain E-pAEAKaG produced 3.21 ± 0.10 g/L 2-phenylethanol in M9 medium containing 10 g/L l-phenylalanine after a 16 h transformation. Furthermore, when the concentration of l-phenylalanine was 4 g/L (24 mM), the production of 2-phenylethanol reached 2.88 ± 0.18 g/L and displayed a higher conversion rate of 97.38 mol %.
Collapse
Affiliation(s)
- Jinbin Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , 1800 Lihu Road , Wuxi , Jiangsu 214122 , China
| | - Jing Jiang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , 1800 Lihu Road , Wuxi , Jiangsu 214122 , China
| | - Yajun Bai
- College of Life Sciences , Northwest University , Xi'an , Shanxi 710069 , China
| | - Tai-Ping Fan
- Department of Pharmacology , University of Cambridge , Cambridge CB2 1T , U.K
| | - Ye Zhao
- College of Life Sciences , Northwest University , Xi'an , Shanxi 710069 , China
| | - Xiaohui Zheng
- College of Life Sciences , Northwest University , Xi'an , Shanxi 710069 , China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , 1800 Lihu Road , Wuxi , Jiangsu 214122 , China
| |
Collapse
|
60
|
Imasaki T, Wenzel S, Yamada K, Bryant ML, Takagi Y. Titer estimation for quality control (TEQC) method: A practical approach for optimal production of protein complexes using the baculovirus expression vector system. PLoS One 2018; 13:e0195356. [PMID: 29614134 PMCID: PMC5882171 DOI: 10.1371/journal.pone.0195356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
The baculovirus expression vector system (BEVS) is becoming the method of choice for expression of many eukaryotic proteins and protein complexes for biochemical, structural and pharmaceutical studies. Significant technological advancement has made generation of recombinant baculoviruses easy, efficient and user-friendly. However, there is a tremendous variability in the amount of proteins made using the BEVS, including different batches of virus made to express the same proteins. Yet, what influences the overall production of proteins or protein complexes remains largely unclear. Many downstream applications, particularly protein structure determination, require purification of large quantities of proteins in a repetitive manner, calling for a reliable experimental set-up to obtain proteins or protein complexes of interest consistently. During our investigation of optimizing the expression of the Mediator Head module, we discovered that the ‘initial infectivity’ was an excellent indicator of overall production of protein complexes. Further, we show that this initial infectivity can be mathematically described as a function of multiplicity of infection (MOI), correlating recombinant protein yield and virus titer. All these findings led us to develop the Titer Estimation for Quality Control (TEQC) method, which enables researchers to estimate initial infectivity, titer/MOI values in a simple and affordable way, and to use these values to quantitatively optimize protein expressions utilizing BEVS in a highly reproducible fashion.
Collapse
Affiliation(s)
- Tsuyoshi Imasaki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Kentaro Yamada
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Megan L. Bryant
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
| |
Collapse
|
61
|
Berlec A, Škrlec K, Kocjan J, Olenic M, Štrukelj B. Single plasmid systems for inducible dual protein expression and for CRISPR-Cas9/CRISPRi gene regulation in lactic acid bacterium Lactococcus lactis. Sci Rep 2018; 8:1009. [PMID: 29343791 PMCID: PMC5772564 DOI: 10.1038/s41598-018-19402-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/29/2017] [Indexed: 12/17/2022] Open
Abstract
Lactococcus lactis is a food-grade lactic acid bacterium that is used in the dairy industry as a cell factory and as a host for recombinant protein expression. The nisin-controlled inducible expression (NICE) system is frequently applied in L. lactis; however new tools for its genetic modification are highly desirable. In this work NICE was adapted for dual protein expression. Plasmid pNZDual, that contains two nisin promoters and multiple cloning sites (MCSs), and pNZPolycist, that contains a single nisin promoter and two MCSs separated by the ribosome binding site, were constructed. Genes for the infrared fluorescent protein and for the human IgG-binding DARPin were cloned in all possible combinations to assess the protein yield. The dual promoter plasmid pNZDual enabled balanced expression of the two model proteins. It was exploited for the development of a single-plasmid inducible CRISPR-Cas9 system (pNZCRISPR) by using a nisin promoter, first to drive Cas9 expression and, secondly, to drive single guide RNA transcription. sgRNAs against htrA and ermR directed Cas9 against genomic or plasmid DNA and caused changes in bacterial growth and survival. Replacing Cas9 by dCas9 enabled CRISPR interference-mediated silencing of the upp gene. The present study introduces a new series of plasmids for advanced genetic modification of lactic acid bacterium L. lactis.
Collapse
Affiliation(s)
- Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia.
| | - Katja Škrlec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Janja Kocjan
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000, Ljubljana, Slovenia
| | - Maria Olenic
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Faculty of Pharmacy, Charles University in Prague, 500 05, Hradec Králové, Czech Republic
| | - Borut Štrukelj
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000, Ljubljana, Slovenia
| |
Collapse
|
62
|
A Small Periplasmic Protein with a Hydrophobic C-Terminal Residue Enhances DegP Proteolysis as a Suicide Activator. J Bacteriol 2018; 200:JB.00519-17. [PMID: 28947671 DOI: 10.1128/jb.00519-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/15/2017] [Indexed: 11/20/2022] Open
Abstract
DegP is a highly conserved protease that performs regulated proteolysis to selectively remove misfolded proteins in the periplasm of Escherichia coli Binding of misfolded proteins is known to be the main mechanism of DegP activation, but it is unknown whether any native proteins can alter DegP activity. Here, we show that a small periplasmic protein, YjfN, which is highly upregulated by the Cpx envelope stress response, functions as a "suicide activator" for DegP and promotes efficient degradation of misfolded proteins. YjfN readily binds to and is degraded by DegP, for which a hydrophobic C-terminal residue and transient unfolding of YjfN are critical. YjfN also activates DegP in trans while it is being degraded and accelerates degradation of a denatured outer membrane protein, OmpA, that is not easily recognized by DegP. Although YjfN also prevents OmpA aggregation, the trans-activation effect is mainly responsible for efficient OmpA degradation. Overexpression of YjfN enhances the viability of cells in misfolded protein stress that is induced by the presence of a less-active variant of DegP at high temperature. Collectively, we suggest that YjfN can enhance DegP proteolysis for relieving envelope stresses that may generate toxic misfolded proteins.IMPORTANCE Proper degradation of toxic misfolded proteins is essential for bacterial survival. This function is mainly performed by a highly conserved protease, DegP, in the periplasm of Escherichia coli It is known that binding of misfolded proteins is the main mechanism for activating the DegP protease. Here, we find that a small periplasmic protein, YjfN, can be a substrate and an activator of DegP. It is the first example of a native protein showing an ability to directly alter DegP activity. The YjfN-mediated trans activation of DegP promotes efficient degradation of misfolded proteins. Our results suggest that YjfN is a novel "suicide activator" for DegP that enhances DegP proteolysis under misfolded protein stress.
Collapse
|
63
|
Goldbeck O, Seibold GM. Construction of pOGOduet - An inducible, bicistronic vector for synthesis of recombinant proteins in Corynebacterium glutamicum. Plasmid 2018; 95:11-15. [PMID: 29331350 DOI: 10.1016/j.plasmid.2018.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 01/14/2023]
Abstract
The Gram-positive Corynebacterium glutamicum is widely known for its application in the industrial production of amino acids and as a non-pathogenic model organism for cell wall biosynthesis in the group of CMN bacteria. For biotechnological and physiological studies often co-expression of recombinant genes is required, however for C. glutamicum no vector for the independent co-expression of two genes was described. We here created the novel expression vector pOGOduet for C. glutamicum, which carries the ColE1 replicon of E. coli and the pBL1 replicon of C. glutamicum and two independently inducible promoters Ptac and Ptet each followed by unique multiple cloning sites. Functionality of pOGOduet is tested by coexpression of genes for the fluorescent proteins eCFP and mVenus; fluorescence of the reporters varies in dependence of the inducer concentrations present in the culture broth. These experiments demonstrate that the vector pOGOduet fulfills the task for individually inducible expression of two genes of interest in C. glutamicum.
Collapse
Affiliation(s)
- Oliver Goldbeck
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Gerd M Seibold
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany.
| |
Collapse
|
64
|
Wu W, Liu F, Davis RW. Engineering Escherichia coli for the production of terpene mixture enriched in caryophyllene and caryophyllene alcohol as potential aviation fuel compounds. Metab Eng Commun 2018; 6:13-21. [PMID: 29349039 PMCID: PMC5767561 DOI: 10.1016/j.meteno.2018.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 12/23/2017] [Accepted: 01/02/2018] [Indexed: 11/26/2022] Open
Abstract
Recent studies have revealed that caryophyllene and its stereoisomers not only exhibit multiple biological activities but also have desired properties as renewable candidates for ground transportation and jet fuel applications. This study presents the first significant production of caryophyllene and caryolan-1-ol by an engineered E. coli with heterologous expression of mevalonate pathway genes with a caryophyllene synthase and a caryolan-1-ol synthase. By optimizing metabolic flux and fermentation parameters, the engineered strains yielded 449 mg/L of total terpene, including 406 mg/L sesquiterpene with 100 mg/L caryophyllene and 10 mg/L caryolan-1-ol. Furthermore, a marine microalgae hydrolysate was used as the sole carbon source for the production of caryophyllene and other terpene compounds. Under the optimal fermentation conditions, 360 mg/L of total terpene, 322 mg/L of sesquiterpene, and 75 mg/L caryophyllene were obtained from the pretreated algae hydrolysates. The highest yields achieved on the biomass basis were 48 mg total terpene/g algae and 10 mg caryophyllene/g algae and the caryophyllene yield is approximately ten times higher than that from plant tissues by solvent extraction. The study provides a sustainable alternative for production of caryophyllene and its alcohol from microalgae biomass as potential candidates for next generation aviation fuels. E. coli was engineered to yield terpene enriched in caryophyllene and caryolan-1-ol. Yields were improved through metabolic flux and culture parameters optimization. Algae hydrolysate was converted to terpene at high yields using engineered strains.
Collapse
Affiliation(s)
- Weihua Wu
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
| | - Fang Liu
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
| | - Ryan W Davis
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
| |
Collapse
|
65
|
Kaur J, Kumar A, Kaur J. Strategies for optimization of heterologous protein expression in E. coli: Roadblocks and reinforcements. Int J Biol Macromol 2018; 106:803-822. [DOI: 10.1016/j.ijbiomac.2017.08.080] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/02/2017] [Accepted: 08/12/2017] [Indexed: 12/29/2022]
|
66
|
Kaur J, Kumar A, Kaur J. Strategies for optimization of heterologous protein expression in E. coli: Roadblocks and reinforcements. Int J Biol Macromol 2018. [DOI: 10.1016/j.ijbiomac.2017.08.080 10.1242/jeb.069716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
67
|
Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
|
68
|
Solid-Phase Agar Plate Assay for Screening Amine Transaminases. Methods Mol Biol 2017. [PMID: 29086316 DOI: 10.1007/978-1-4939-7366-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Agar plate assays represent a useful method for high-throughput prescreening of larger enzyme libraries derived from for example error-prone PCR or multiple site-saturation mutagenesis to decrease screening effort by separating promising variants from less active, inactive, or neutral variants. In order to do so, colonies are directly applied for enzyme expression and screening on adsorbent and microporous membranes instead of elaborately preparing cell lysates in 96-well plates. This way, 400-800 enzyme variants can be prescreened on a single membrane, 10,000-20,000 variants per week and per single researcher respectively (25 membranes per week).The following chapter gives a detailed protocol of how to screen transaminase libraries in solid phase, but it also intends to provide inspiration to establish a direct or coupled agar plate assay for screening variable enzymatic activities by interchanging assay enzymes and adapting assay conditions to individual needs.
Collapse
|
69
|
Guo C, Wu ZL. Construction and functional analysis of a whole-cell biocatalyst based on CYP108N7. Enzyme Microb Technol 2017; 106:28-34. [DOI: 10.1016/j.enzmictec.2017.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022]
|
70
|
Nasiri M, Babaie J, Amiri S, Azimi E, Shamshiri S, Khalaj V, Golkar M, Fard-Esfahani P. SHuffle™ T7 strain is capable of producing high amount of recombinant human fibroblast growth factor-1 (rhFGF-1) with proper physicochemical and biological properties. J Biotechnol 2017; 259:30-38. [PMID: 28827102 DOI: 10.1016/j.jbiotec.2017.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/14/2017] [Accepted: 08/11/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND Human fibroblast growth factor-1 (FGF-1) has powerful mitogenic activities in a variety of cell types and plays significant roles in many physiological processes e.g. angiogenesis and wound healing. There is increasing demand for large scale production of recombinant human FGF-1 (rhFGF-1), in order to investigate the potential medical use. In the present study, we explored SHuffle™ T7 strain for production of rhFGF-1. METHODS A synthetic gene encoding Met-140 amino acid form of human FGF-1 was utilized for expression of the protein in three different E. coli hosts (BL21 (DE3), Rosetta-gami™ 2(DE3), SHuffle™ T7). Total expressions and soluble/insoluble expression ratios of rhFGF-1 in different hosts were analyzed and compared. Soluble rhFGF-1 produced in SHuffle™ T7 cells was purified using one-step heparin-Sepharose affinity chromatography and characterized by a variety of methods for physicochemical and biological properties. RESULTS The highest level of rhFGF-1 expression and maximum soluble/insoluble ratio were achieved in SHuffle™ T7 strain. Using a single-step heparin-Sepharose chromatography, about 1500mg of purified rhFGF-1 was obtained from one liter of the culture, representing purification yield of ∼70%. The purified protein was reactive toward anti-FGF-1 ployclonal antibody in immunoblotting. Mass spectrometry confirmed the protein had expected amino acid sequence and molecular weight. In reverse-phase high-performance liquid chromatography (RP-HPLC), the protein displayed the same retention time with the human FGF-1 standard, and purity of 94%. Less than 0.3% of the purified protein was comprised of oligomers and/or aggregates as judged by high-performance size-exclusion chromatography (HP-SEC). Secondary and tertiary structures of the protein, investigated by circular dichroism and intrinsic fluorescence spectroscopy methods, respectively, represented native folding of the protein. The purified rhFGF-1 was bioactive and stimulated proliferation of NIH 3T3 cells with EC50 of 0.84ng/mL. CONCLUSION Although SHuffle™ T7 has been introduced for production of disulfide-bonded proteins in cytoplasm, we herein successfully recruited it for high yield production of soluble and bioactive rhFGF-1, a protein with 3 free cysteine and no disulfide bond. To our knowledge, this is the highest-level of rhFGF-1 expression in E. coli reported so far. Extensive physicochemical and biological analysis showed the protein had similar characteristic to authentic FGF-1.
Collapse
Affiliation(s)
- Marzieh Nasiri
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran; Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran.
| | - Jalal Babaie
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran.
| | - Samira Amiri
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran.
| | - Ebrahim Azimi
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran.
| | - Shiva Shamshiri
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran.
| | - Vahid Khalaj
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Iran.
| | - Majid Golkar
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran.
| | | |
Collapse
|
71
|
da Silva AF, García-Fraga B, López-Seijas J, Sieiro C. Optimizing the expression of a Heterologous chitinase: A study of different promoters. Bioengineered 2017; 8:428-432. [PMID: 27893301 DOI: 10.1080/21655979.2016.1249074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Many relevant applications have been demonstrated for chitinolytic enzymes. However, their successful exploitation depends upon the availability of strains and expression conditions that allow the production of active forms and large quantities of these enzymes. Escherichia coli has been commonly used to express and overproduce different proteins, among them chitinases. Improving the functional gene expression of chitinases is key to exploiting their potential. In a recent study, we described the effect of various parameters on the functional expression of 2 chitinases from different families, demonstrating that the effect of each of these parameters on the activity of both chitinases was specific to each enzyme. In this study, the expression of a Lactococcus lactis chitinase encoded by a new allele, ChiA1-2, was optimized. The results showed that not only the expression parameters seemed to influence protein production, solubility and activity but also the plasmid used for the expression. Herein, we describe the effect of 2 different promoters, tac and T7, on the expression of the active form of the chitinolytic enzyme.
Collapse
Affiliation(s)
- Abigail F da Silva
- a Department of Functional Biology and Health Sciences , Microbiology Area, University of Vigo, Lagoas - Marcosende , Vigo , Spain
| | - Belén García-Fraga
- a Department of Functional Biology and Health Sciences , Microbiology Area, University of Vigo, Lagoas - Marcosende , Vigo , Spain
| | - Jacobo López-Seijas
- a Department of Functional Biology and Health Sciences , Microbiology Area, University of Vigo, Lagoas - Marcosende , Vigo , Spain
| | - Carmen Sieiro
- a Department of Functional Biology and Health Sciences , Microbiology Area, University of Vigo, Lagoas - Marcosende , Vigo , Spain
| |
Collapse
|
72
|
Ashkani J, Rees DJG. Selecting an appropriate method for expressing S locus F-box-S2 recombinant protein. ACTA ACUST UNITED AC 2017; 15:41-47. [PMID: 28664149 PMCID: PMC5480281 DOI: 10.1016/j.btre.2017.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/27/2017] [Accepted: 06/15/2017] [Indexed: 11/23/2022]
Abstract
Understanding the molecular basis of self-incompatibility (SI) is essential for commercial production of fruit crops such as Apple. To investigate the molecular interactions in self-incompatibility locus (Slocus), the knowledge of tertiary structures of both male (i.e. S-locus F-box) and female (i.e. SRNase) proteins are necessary. The tertiary structure of male determinant (S locus F-box, SLF/SFB) remains unresolved, which could mainly be due to difficulties associated with its expression in the recombinant expression systems. This study demonstrates an approach for efficient expression of S locus F-box recombinant proteins for future functional and structural studies.
A single locus (S locus) including at least two linked genes (female and male determinants) genetically controls the gametophytic self-incompatibility (GSI) in apple, which has evolved to avoid self-fertilization. There has been extensive work done on the female determinant of self-incompatibility, which has led to the determination of the tertiary structure of S-RNase. However, the tertiary structure of male determinant (S locus F-box, SLF/SFB) remains unresolved, which could mainly be due to difficulties associated with its expression in the recombinant expression systems. In addressing this, we have evaluated several in vivo (prokaryotic and eukaryotic) and in vitro expression systems for their efficiency in the expression of apple SLF2. The most successful expression of SLF2 (1 mg/ml) was achieved in E. coli using the synthesized gene in a high salt culture and applying heat shock before induction of culture. We therefore present an approach for the efficient expression of S locus F-box recombinant proteins for future functional and structural studies.
Collapse
Affiliation(s)
- Jahanshah Ashkani
- Biotechnology Department, University of the Western Cape, Robert Sobokwe Road, Bellville, 7535, South Africa.,Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa
| | - D J G Rees
- Biotechnology Department, University of the Western Cape, Robert Sobokwe Road, Bellville, 7535, South Africa.,Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa
| |
Collapse
|
73
|
Hassan MI, McSorley FR, Hotta K, Boddy CN. Inducible T7 RNA Polymerase-mediated Multigene Expression System, pMGX. J Vis Exp 2017. [PMID: 28715370 DOI: 10.3791/55187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Co-expression of multiple proteins is increasingly essential for synthetic biology, studying protein-protein complexes, and characterizing and harnessing biosynthetic pathways. In this manuscript, the use of a highly effective system for the construction of multigene synthetic operons under the control of an inducible T7 RNA polymerase is described. This system allows many genes to be expressed simultaneously from one plasmid. Here, a set of four related vectors, pMGX-A, pMGX-hisA, pMGX-K, and pMGX-hisK, with either the ampicillin or kanamycin resistance selectable marker (A and K) and either possessing or lacking an N-terminal hexahistidine tag (his) are disclosed. Detailed protocols for the construction of synthetic operons using this vector system are provided along with the corresponding data, showing that a pMGX-based system containing five genes can be readily constructed and used to produce all five encoded proteins in Escherichia coli. This system and protocol enables researchers to routinely express complex multi-component modules and pathways in E. coli.
Collapse
Affiliation(s)
- Mohamed I Hassan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa
| | - Fern R McSorley
- Department of Chemistry and Biomolecular Sciences, University of Ottawa
| | - Kinya Hotta
- School of Biosciences, The University of Nottingham Malaysia Campus;
| | | |
Collapse
|
74
|
Chen H, Huang R, Zhang YHP. Systematic comparison of co-expression of multiple recombinant thermophilic enzymes in Escherichia coli BL21(DE3). Appl Microbiol Biotechnol 2017; 101:4481-4493. [PMID: 28251267 DOI: 10.1007/s00253-017-8206-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 01/08/2023]
Abstract
The precise control of multiple heterologous enzyme expression levels in one Escherichia coli strain is important for cascade biocatalysis, metabolic engineering, synthetic biology, natural product synthesis, and studies of complexed proteins. We systematically investigated the co-expression of up to four thermophilic enzymes (i.e., α-glucan phosphorylase (αGP), phosphoglucomutase (PGM), glucose 6-phosphate dehydrogenase (G6PDH), and 6-phosphogluconate dehydrogenase (6PGDH)) in E. coli BL21(DE3) by adding T7 promoter or T7 terminator of each gene for multiple genes in tandem, changing gene alignment, and comparing one or two plasmid systems. It was found that the addition of T7 terminator after each gene was useful to decrease the influence of the upstream gene. The co-expression of the four enzymes in E. coli BL21(DE3) was demonstrated to generate two NADPH molecules from one glucose unit of maltodextrin, where NADPH was oxidized to convert xylose to xylitol. The best four-gene co-expression system was based on two plasmids (pET and pACYC) which harbored two genes. As a result, apparent enzymatic activities of the four enzymes were regulated to be at similar levels and the overall four-enzyme activity was the highest based on the formation of xylitol. This study provides useful information for the precise control of multi-enzyme-coordinated expression in E. coli BL21(DE3).
Collapse
Affiliation(s)
- Hui Chen
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA
| | - Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
| |
Collapse
|
75
|
Optimization of culturing conditions of recombined Escherichia coli to produce umami octopeptide-containing protein. Food Chem 2017; 227:78-84. [PMID: 28274461 DOI: 10.1016/j.foodchem.2017.01.096] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/17/2016] [Accepted: 01/17/2017] [Indexed: 12/24/2022]
Abstract
Using synthesized peptides to verify the taste of natural peptides was probably the leading cause for tasting disputes regarding umami peptides. A novel method was developed to prepare the natural peptide which could be used to verify the taste of umami peptide. A controversial octopeptide was selected and gene engineering was used to structure its Escherichia coli. expressing vector. A response surface method was adopted to optimize the expression conditions of the recombinant protein. The results of SDS-PAGE for the recombinant protein indicated that the recombinant expression system was successfully structured. The fitting results of the response surface experiment showed that the OD600 value was the key factor which influenced the expression of the recombinant protein. The optimal culturing process conditions predicted with the fitting model were an OD600 value of 0.5, an IPTG concentration of 0.6mM, a culturing temperature of 28.75°C and a culturing time of 5h.
Collapse
|
76
|
Dziggel C, Schäfer H, Wink M. Tools of pathway reconstruction and production of economically relevant plant secondary metabolites in recombinant microorganisms. Biotechnol J 2016; 12. [DOI: 10.1002/biot.201600145] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/28/2016] [Accepted: 11/29/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Clarissa Dziggel
- Heidelberg University; Institute of Pharmacy and Molecular Biotechnology; Heidelberg Germany
| | - Holger Schäfer
- Heidelberg University; Institute of Pharmacy and Molecular Biotechnology; Heidelberg Germany
| | - Michael Wink
- Heidelberg University; Institute of Pharmacy and Molecular Biotechnology; Heidelberg Germany
| |
Collapse
|
77
|
Tryptophan tags and de novo designed complementary affinity ligands for the expression and purification of recombinant proteins. J Chromatogr A 2016; 1472:55-65. [DOI: 10.1016/j.chroma.2016.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/29/2016] [Accepted: 10/08/2016] [Indexed: 01/05/2023]
|
78
|
Hong TJ, Hahn JS. Application of SGT1-Hsp90 chaperone complex for soluble expression of NOD1 LRR domain in E. coli. Biochem Biophys Res Commun 2016; 478:1647-52. [PMID: 27591899 DOI: 10.1016/j.bbrc.2016.08.174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 08/30/2016] [Indexed: 12/17/2022]
Abstract
NOD1 is an intracellular sensor of innate immunity which is related to a number of inflammatory diseases. NOD1 is known to be difficult to express and purify for structural and biochemical studies. Based on the fact that Hsp90 and its cochaperone SGT1 are necessary for the stabilization and activation of NOD1 in mammals, SGT1 was chosen as a fusion partner of the leucine-rich repeat (LRR) domain of NOD1 for its soluble expression in Escherichia coli. Fusion of human SGT1 (hSGT1) to NOD1 LRR significantly enhanced the solubility, and the fusion protein was stabilized by coexpression of mouse Hsp90α. The expression level of hSGT1-NOD1 LRR was further enhanced by supplementation of rare codon tRNAs and exchange of antibiotic marker genes.
Collapse
Affiliation(s)
- Tae-Joon Hong
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
| |
Collapse
|
79
|
Optimized expression conditions for enhancing production of two recombinant chitinolytic enzymes from different prokaryote domains. Bioprocess Biosyst Eng 2016; 38:2477-86. [PMID: 26470707 DOI: 10.1007/s00449-015-1485-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
Enhancing functional gene expression is key to high-level production of active chitinases. For this purpose, the effects of culture cell density, inducer concentration, post-induction time and induction temperatures on the functional expression of two different chitinases (HsChiA1p, a family 18 archaeal chitinase and PtChi19p, a family 19 bacterial chitinase) were comparatively investigated. Results showed that the effect of each parameter on the activity of both chitinases was specific to each enzyme. In addition, different Escherichia coli host strains compatible with the expression in pET systems were assayed for active protein overexpression. When using BL21 Star (DE3), a significant increase of 60% in expression was observed for the active archaeal chitinase HsChiA1p as compared to that found when using BL21 (DE3), indicating that the rne131 gene mutation efficiently stabilizes the mRNA for HsChiA1p. Using the Codon Adaptation Index value, rare codon analysis of the archaeal HschiA1 and bacterial Ptchi19 genes revealed that both DNA sequences were not optimal for maximal expression in E. coli. Different E. coli host strains possess extra copies of some of the tRNA genes for rare codons. For the Rosetta 2 (DE3) and the BL21 RP (DE3) strains, a significant increase of 40% was reached for the activity of HsChiA1p and PtChi19p. Finally, as part of the protein still remained insoluble, the best conditions for recovering biologically active protein from inclusion bodies were established for each enzyme.
Collapse
|
80
|
Construction of a tunable multi-enzyme-coordinate expression system for biosynthesis of chiral drug intermediates. Sci Rep 2016; 6:30462. [PMID: 27456301 PMCID: PMC4960608 DOI: 10.1038/srep30462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Systems that can regulate and coordinate the expression of multiple enzymes for metabolic regulation and synthesis of important drug intermediates are poorly explored. In this work, a strategy for constructing a tunable multi-enzyme-coordinate expression system for biosynthesis of chiral drug intermediates was developed and evaluated by connecting protein-protein expressions, regulating the strength of ribosome binding sites (RBS) and detecting the system capacity for producing chiral amino acid. Results demonstrated that the dual-enzyme system had good enantioselectivity, low cost, high stability, high conversion rate and approximately 100% substrate conversion. This study has paved a new way of exploring metabolic mechanism of functional genes and engineering whole cell-catalysts for synthesis of chiral α-hydroxy acids or chiral amino acids.
Collapse
|
81
|
Masuo S, Zhou S, Kaneko T, Takaya N. Bacterial fermentation platform for producing artificial aromatic amines. Sci Rep 2016; 6:25764. [PMID: 27167511 PMCID: PMC4863162 DOI: 10.1038/srep25764] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/21/2016] [Indexed: 12/03/2022] Open
Abstract
Aromatic amines containing an aminobenzene or an aniline moiety comprise versatile natural and artificial compounds including bioactive molecules and resources for advanced materials. However, a bio-production platform has not been implemented. Here we constructed a bacterial platform for para-substituted aminobenzene relatives of aromatic amines via enzymes in an alternate shikimate pathway predicted in a Pseudomonad bacterium. Optimization of the metabolic pathway in Escherichia coli cells converted biomass glucose to 4-aminophenylalanine with high efficiency (4.4 g L−1 in fed-batch cultivation). We designed and produced artificial pathways that mimicked the fungal Ehrlich pathway in E. coli and converted 4-aminophenylalanine into 4-aminophenylethanol and 4-aminophenylacetate at 90% molar yields. Combining these conversion systems or fungal phenylalanine decarboxylases, the 4-aminophenylalanine-producing platform fermented glucose to 4-aminophenylethanol, 4-aminophenylacetate, and 4-phenylethylamine. This original bacterial platform for producing artificial aromatic amines highlights their potential as heteroatoms containing bio-based materials that can replace those derived from petroleum.
Collapse
Affiliation(s)
- Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shengmin Zhou
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Tatsuo Kaneko
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292 Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| |
Collapse
|
82
|
Mirza N, Crocoll C, Erik Olsen C, Ann Halkier B. Engineering of methionine chain elongation part of glucoraphanin pathway in E. coli. Metab Eng 2016; 35:31-37. [DOI: 10.1016/j.ymben.2015.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 07/24/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
|
83
|
Giordano D, Provenzano S, Ferrandino A, Vitali M, Pagliarani C, Roman F, Cardinale F, Castellarin SD, Schubert A. Characterization of a multifunctional caffeoyl-CoA O-methyltransferase activated in grape berries upon drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 101:23-32. [PMID: 26851572 DOI: 10.1016/j.plaphy.2016.01.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/12/2016] [Accepted: 01/19/2016] [Indexed: 05/25/2023]
Abstract
Drought stress affects anthocyanin accumulation and modification in vegetative and reproductive plant tissues. Anthocyanins are the most abundant flavonoids in grape (Vitis vinifera L.) coloured berry genotypes and are essential markers of grape winemaking quality. They are mostly mono- and di-methylated, such modifications increase their stability and improve berry quality for winemaking. Anthocyanin methylation in grape berries is induced by drought stress. A few caffeoyl-CoA O-methyltransferases (CCoAOMTs) active on anthocyanins have been described in grape. However, no drought-activated O-methyltransferases have been described in grape berries yet. In this study, we characterized VvCCoAOMT, a grapevine gene known to induce methylation of CoA esters in cultured grape cells. Transcript accumulation of VvCCoAOMT was detected in berry skins, and increased during berry ripening on the plant, and in cultured berries treated with ABA, concomitantly with accumulation of methylated anthocyanins, suggesting that anthocyanins may be substrates of this enzyme. Contrary as previously observed in cell cultures, biotic stress (Botrytis cinerea inoculation) did not affect VvCCoAOMT gene expression in leaves or berries, while drought stress increased VvCCoAOMT transcript in berries. The recombinant VvCCoAOMT protein showed in vitro methylating activity on cyanidin 3-O-glucoside. We conclude that VvCCoAOMT is a multifunctional O-methyltransferase that may contribute to anthocyanin methylation activity in grape berries, in particular under drought stress conditions.
Collapse
Affiliation(s)
- Debora Giordano
- University of Turin, Dept. Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy
| | - Sofia Provenzano
- University of Turin, Dept. Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy
| | - Alessandra Ferrandino
- University of Turin, Dept. Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy
| | - Marco Vitali
- University of Turin, Dept. Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy
| | - Chiara Pagliarani
- University of Turin, Dept. Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy
| | - Federica Roman
- University of Turin, Dept. Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy
| | - Francesca Cardinale
- University of Turin, Dept. Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy
| | - Simone D Castellarin
- The University of British Columbia Wine Research Centre, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Andrea Schubert
- University of Turin, Dept. Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy.
| |
Collapse
|
84
|
Willies SC, Galman JL, Slabu I, Turner NJ. A stereospecific solid-phase screening assay for colonies expressing both (R)- and (S)-selective ω-aminotransferases. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0084. [PMID: 26755753 DOI: 10.1098/rsta.2015.0084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/08/2015] [Indexed: 06/05/2023]
Abstract
A novel solid-phase screening assay was developed for colonies expressing both (R)- and (S)-selective ω-aminotransferases. This high-throughput assay can be used to screen rapidly large variant libraries with enhanced substrate selectivity and enantioselectivities.
Collapse
Affiliation(s)
- Simon C Willies
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - James L Galman
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Iustina Slabu
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Nicholas J Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| |
Collapse
|
85
|
Bergamin E, Couture JF. Preparation, Biochemical Analysis, and Structure Determination of SET Domain Histone Methyltransferases. Methods Enzymol 2016; 573:209-40. [PMID: 27372755 DOI: 10.1016/bs.mie.2016.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In eukaryotes, several lysine residues on histone proteins are methylated. This posttranslational modification is linked to a myriad of nuclear-based transactions such as epigenetic inheritance of heterochromatin, regulation of gene expression, DNA damage repair, and DNA replication. The majority of the enzymes responsible for writing these marks onto chromatin belong to the SET domain family of histone lysine methyltransferases. Although they often share important structural features, including a conserved catalytic domain, SET domain enzymes use different mechanisms to achieve substrate recognition, mono-, di-, or trimethylate lysine residues and some require other proteins to achieve maximal methyltransferase activity. In this chapter, we summarize our efforts to purify, crystallize, and enzymatically characterize SET domain enzymes with a specific focus on the histone H3K27 monomethyltransferase ATXR5.
Collapse
Affiliation(s)
- E Bergamin
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - J F Couture
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.
| |
Collapse
|
86
|
Vincentelli R, Romier C. Complex Reconstitution and Characterization by Combining Co-expression Techniques in Escherichia coli with High-Throughput. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:43-58. [PMID: 27165318 DOI: 10.1007/978-3-319-27216-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Single protein expression technologies have strongly benefited from the Structural Genomics initiatives that have introduced parallelization at the laboratory level. Specifically, the developments made in the wake of these initiatives have revitalized the use of Escherichia coli as major host for heterologous protein expression. In parallel to these improvements for single expression, technologies for complex reconstitution by co-expression in E. coli have been developed. Assessments of these co-expression technologies have highlighted the need for combinatorial experiments requiring automated protocols. These requirements can be fulfilled by adapting the high-throughput approaches that have been developed for single expression to the co-expression technologies. Yet, challenges are laying ahead that further need to be addressed and that are only starting to be taken into account in the case of single expression. These notably include the biophysical characterization of the samples at the small-scale level. Specifically, these approaches aim at discriminating the samples at an early stage of their production based on various biophysical criteria leading to cost-effectiveness and time-saving. This chapter addresses these various issues to provide the reader with a broad and comprehensive overview of complex reconstitution and characterization by co-expression in E. coli.
Collapse
Affiliation(s)
- Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques (A.F.M.B), UMR7257 CNRS, Université Aix-Marseille, Case 932, 163 Avenue de Luminy, 13288, Marseille cedex 9, France.
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Centre de Biologie Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France.
| |
Collapse
|
87
|
Pacak A, Barciszewska-Pacak M, Swida-Barteczka A, Kruszka K, Sega P, Milanowska K, Jakobsen I, Jarmolowski A, Szweykowska-Kulinska Z. Heat Stress Affects Pi-related Genes Expression and Inorganic Phosphate Deposition/Accumulation in Barley. FRONTIERS IN PLANT SCIENCE 2016; 7:926. [PMID: 27446155 PMCID: PMC4919326 DOI: 10.3389/fpls.2016.00926] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/10/2016] [Indexed: 05/07/2023]
Abstract
Phosphorus (P) in plants is taken from soil as an inorganic phosphate (Pi) and is one of the most important macroelements in growth and development. Plants actively react to Pi starvation by the induced expression of Pi transporters, MIR399, MIR827, and miR399 molecular sponge - IPS1 genes and by the decreased expression of the ubiquitin-conjugating enzyme E2 (PHOSPHATE2 - PHO2) and Pi sensing and transport SPX-MFS genes. The PHO2 protein is involved in the degradation of Pi transporters PHT1;1 (from soil to roots) and PHO1 (from roots to shoots). The decreased expression of PHO2 leads to Pi accumulation in shoots. In contrast, the pho1 mutant shows a decreased level of Pi concentration in shoots. Finally, Pi starvation leads to decreased Pi concentration in all plant tissues. Little is known about plant Pi homeostasis in other abiotic stress conditions. We found that, during the first hour of heat stress, Pi accumulated in barley shoots but not in the roots, and transcriptomic data analysis as well as RT-qPCR led us to propose an explanation for this phenomenon. Pi transport inhibition from soil to roots is balanced by lower Pi efflux from roots to shoots directed by the PHO1 transporter. In shoots, the PHO2 mRNA level is decreased, leading to an increased Pi level. We concluded that Pi homeostasis in barley during heat stress is maintained by dynamic changes in Pi-related genes expression.
Collapse
Affiliation(s)
- Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
- *Correspondence: Andrzej Pacak,
| | - Maria Barciszewska-Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Pawel Sega
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Kaja Milanowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Iver Jakobsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of CopenhagenCopenhagen, Denmark
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in PoznanPoznan, Poland
| |
Collapse
|
88
|
Dvorak P, Chrast L, Nikel PI, Fedr R, Soucek K, Sedlackova M, Chaloupkova R, de Lorenzo V, Prokop Z, Damborsky J. Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway. Microb Cell Fact 2015; 14:201. [PMID: 26691337 PMCID: PMC4687329 DOI: 10.1186/s12934-015-0393-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 12/05/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Heterologous expression systems based on promoters inducible with isopropyl-β-D-1-thiogalactopyranoside (IPTG), e.g., Escherichia coli BL21(DE3) and cognate LacI(Q)/P(lacUV5)-T7 vectors, are commonly used for production of recombinant proteins and metabolic pathways. The applicability of such cell factories is limited by the complex physiological burden imposed by overexpression of the exogenous genes during a bioprocess. This burden originates from a combination of stresses that may include competition for the expression machinery, side-reactions due to the activity of the recombinant proteins, or the toxicity of their substrates, products and intermediates. However, the physiological impact of IPTG-induced conditional expression on the recombinant host under such harsh conditions is often overlooked. RESULTS The physiological responses to IPTG of the E. coli BL21(DE3) strain and three different recombinants carrying a synthetic metabolic pathway for biodegradation of the toxic anthropogenic pollutant 1,2,3-trichloropropane (TCP) were investigated using plating, flow cytometry, and electron microscopy. Collected data revealed unexpected negative synergistic effect of inducer of the expression system and toxic substrate resulting in pronounced physiological stress. Replacing IPTG with the natural sugar effector lactose greatly reduced such stress, demonstrating that the effect was due to the original inducer's chemical properties. CONCLUSIONS IPTG is not an innocuous inducer; instead, it exacerbates the toxicity of haloalkane substrate and causes appreciable damage to the E. coli BL21(DE3) host, which is already bearing a metabolic burden due to its content of plasmids carrying the genes of the synthetic metabolic pathway. The concentration of IPTG can be effectively tuned to mitigate this negative effect. Importantly, we show that induction with lactose, the natural inducer of P lac , dramatically lightens the burden without reducing the efficiency of the synthetic TCP degradation pathway. This suggests that lactose may be a better inducer than IPTG for the expression of heterologous pathways in E. coli BL21(DE3).
Collapse
Affiliation(s)
- Pavel Dvorak
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Lukas Chrast
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, 28049, Madrid, Spain.
| | - Radek Fedr
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65, Brno, Czech Republic.
| | - Karel Soucek
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65, Brno, Czech Republic.
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.
| | - Miroslava Sedlackova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic.
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, 28049, Madrid, Spain.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| |
Collapse
|
89
|
Integrated Optimization of the In Vivo Heme Biosynthesis Pathway and the In Vitro Iron Concentration for 5-Aminolevulinate Production. Appl Biochem Biotechnol 2015; 178:1252-62. [PMID: 26637361 DOI: 10.1007/s12010-015-1942-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
5-Aminolevulinic acid (ALA) is a nonprotein amino acid that has been widely used in many fields. In this study, we developed a new process for ALA production by optimizing the in vivo heme biosynthesis pathway and the iron concentration during cultivation. With the addition of iron, co-overexpression of the heme synthesis pathway genes hemA, hemL, hemF, and hemD significantly increased the accumulation of ALA and cell biomass. Further experiments demonstrated that the increased ALA accumulation resulted from moderate repression of ALA dehydratase (encoded by hemB), which was caused by hemF overexpression. After the addition of an optimized concentration (7.5 mg/L) of iron, ALA production by the recombinant Escherichia coli LADF-6 strain that overexpressed hemA, hemL, hemD, and hemF increased to 2840 mg/L in flask cultures. After applying a batch fermentation strategy, the ALA concentration increased to 4.05 g/L, with a productivity of 0.127 g/L·h. The results showed that the moderate repression of the in vivo heme pathway enzyme ALA dehydratase and the simultaneous optimization of the in vitro iron ion concentration served to increase the production of ALA and cell biomass.
Collapse
|
90
|
Shariq M, Kumar N, Kumari R, Kumar A, Subbarao N, Mukhopadhyay G. Biochemical Analysis of CagE: A VirB4 Homologue of Helicobacter pylori Cag-T4SS. PLoS One 2015; 10:e0142606. [PMID: 26565397 PMCID: PMC4643968 DOI: 10.1371/journal.pone.0142606] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/23/2015] [Indexed: 12/30/2022] Open
Abstract
Helicobacter pylori are among the most successful human pathogens that harbour a distinct genomic segment called cag Pathogenicity Island (cag-PAI). This genomic segment codes for a type IV secretion system (Cag-T4SS) related to the prototypical VirB/D4 system of Agrobacterium tumefaciens (Ag), a plant pathogen. Some of the components of Cag-T4SS share homology to that of VirB proteins including putative energy providing CagE (HP0544), the largest VirB4 homologue. In Ag, VirB4 is required for the assembly of the system, substrate translocation and pilus formation, however, very little is known about CagE. Here we have characterised the protein biochemically, genetically, and microscopically and report that CagE is an inner membrane associated active NTPase and has multiple interacting partners including the inner membrane proteins CagV and Cagβ. Through CagV it is connected to the outer membrane sub-complex proteins. Stability of CagE is not dependent on several of the cag-PAI proteins tested. However, localisation and stability of the pilus associated CagI, CagL and surface associated CagH are affected in its absence. Stability of the inner membrane associated energetic component Cagβ, a VirD4 homologue seems to be partially affected in its absence. Additionally, CagA failed to cross the membrane barriers in its absence and no IL-8 induction is observed under infection condition. These results thus suggest the importance of CagE in Cag-T4SS functions. In future it may help in deciphering the mechanism of substrate translocation by the system.
Collapse
Affiliation(s)
- Mohd Shariq
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail: (MS); (GM)
| | - Navin Kumar
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Amarjeet Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gauranga Mukhopadhyay
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- * E-mail: (MS); (GM)
| |
Collapse
|
91
|
Shin J, Jung YH, Cho DH, Park M, Lee KE, Yang Y, Jeong C, Sung BH, Sohn JH, Park JB, Kweon DH. Display of membrane proteins on the heterologous caveolae carved by caveolin-1 in the Escherichia coli cytoplasm. Enzyme Microb Technol 2015; 79-80:55-62. [DOI: 10.1016/j.enzmictec.2015.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/20/2015] [Accepted: 06/26/2015] [Indexed: 11/25/2022]
|
92
|
Morra S, Cordara A, Gilardi G, Valetti F. Atypical effect of temperature tuning on the insertion of the catalytic iron-sulfur center in a recombinant [FeFe]-hydrogenase. Protein Sci 2015; 24:2090-4. [PMID: 26362685 DOI: 10.1002/pro.2805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 01/04/2023]
Abstract
The expression of recombinant [FeFe]-hydrogenases is an important step for the production of large amount of these enzymes for their exploitation in biotechnology and for the characterization of the protein-metal cofactor interactions. The correct assembly of the organometallic catalytic site, named H-cluster, requires a dedicated set of maturases that must be coexpressed in the microbial hosts or used for in vitro assembly of the active enzymes. In this work, the effect of the post-induction temperature on the recombinant expression of CaHydA [FeFe]-hydrogenase in E. coli is investigated. The results show a peculiar behavior: the enzyme expression is maximum at lower temperatures (20°C), while the specific activity of the purified CaHydA is higher at higher temperature (30°C), as a consequence of improved protein folding and active site incorporation.
Collapse
Affiliation(s)
- Simone Morra
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Alessandro Cordara
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| |
Collapse
|
93
|
Gourinchas G, Busto E, Killinger M, Richter N, Wiltschi B, Kroutil W. A synthetic biology approach for the transformation of l-α-amino acids to the corresponding enantiopure (R)- or (S)-α-hydroxy acids. Chem Commun (Camb) 2015; 51:2828-31. [PMID: 25574527 DOI: 10.1039/c4cc08286a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Combinatorial assembly and variation of promoters on a single expression plasmid allowed the balance of the catalytic steps of a three enzyme (l-AAD, HIC, FDH) cascade in E. coli. The designer cell catalyst quantitatively transformed l-amino acids to the corresponding optically pure (R)- and (S)-α-hydroxy acids at up to 200 mM substrate concentration.
Collapse
Affiliation(s)
- Geoffrey Gourinchas
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria.
| | | | | | | | | | | |
Collapse
|
94
|
Kratzer R, Woodley JM, Nidetzky B. Rules for biocatalyst and reaction engineering to implement effective, NAD(P)H-dependent, whole cell bioreductions. Biotechnol Adv 2015; 33:1641-52. [PMID: 26343336 PMCID: PMC5414839 DOI: 10.1016/j.biotechadv.2015.08.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/21/2015] [Accepted: 08/31/2015] [Indexed: 12/27/2022]
Abstract
Access to chiral alcohols of high optical purity is today frequently provided by the enzymatic reduction of precursor ketones. However, bioreductions are complicated by the need for reducing equivalents in the form of NAD(P)H. The high price and molecular weight of NAD(P)H necessitate in situ recycling of catalytic quantities, which is mostly accomplished by enzymatic oxidation of a cheap co-substrate. The coupled oxidoreduction can be either performed by free enzymes in solution or by whole cells. Reductase selection, the decision between cell-free and whole cell reduction system, coenzyme recycling mode and reaction conditions represent design options that strongly affect bioreduction efficiency. In this paper, each option was critically scrutinized and decision rules formulated based on well-described literature examples. The development chain was visualized as a decision-tree that can be used to identify the most promising route towards the production of a specific chiral alcohol. General methods, applications and bottlenecks in the set-up are presented and key experiments required to "test" for decision-making attributes are defined. The reduction of o-chloroacetophenone to (S)-1-(2-chlorophenyl)ethanol was used as one example to demonstrate all the development steps. Detailed analysis of reported large scale bioreductions identified product isolation as a major bottleneck in process design.
Collapse
Affiliation(s)
- Regina Kratzer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria.
| | - John M Woodley
- CAPEC-PROCESS Research Center, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 229, 2800 Kgs. Lyngby, Denmark.
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria.
| |
Collapse
|
95
|
Ganapathy M, Chakravarthi M, Charles SJ, Harunipriya P, Jaiganesh S, Subramonian N, Kaliraj P. Immunodiagnostic Properties of Wucheraria bancrofti SXP-1, a Potential Filarial Diagnostic Candidate Expressed in Tobacco Plant, Nicotiana tabacum. Appl Biochem Biotechnol 2015; 176:1889-903. [PMID: 26043851 DOI: 10.1007/s12010-015-1685-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/25/2015] [Indexed: 11/28/2022]
Abstract
Transgenic tobacco plants were developed expressing WbSXP-1, a diagnostic antigen isolated from the cDNA library of L3 stage larvae of Wucheraria bancrofti. This antigen produced by recombinant Escherichia coli has been demonstrated by to be successful as potential diagnostic candidate against lymphatic filariasis. A rapid format simple and qualitative flow through immune-filtration diagnostic kit has been developed for the identification of IgG antibodies to the recombinant WbSXP-1 and is being marketed by M/S Span Diagnostics Ltd in India and Africa. Here, we present the results of experiments on the transformation and expression of the same filarial antigen, WbSXP-1, in tobacco plant, Nicotiana tabacum, to produce plant-based diagnostic antigen. It was possible to successfully transform the tobacco plant with WbSXP-1, the integration of the parasite-specific gene in plants was confirmed by PCR amplification and the expression of the filarial protein by Western blotting. The immunoreactivity of the plant-produced WbSXP-1 was assessed based on its reaction with the monoclonal antibodies developed against the E. coli-produced protein. Immunological screening using clinical sera from patients indicates that the plant-produced protein is comparable to E. coli-produced diagnostic antigen. The result demonstrated that plants can be used as suitable expression systems for the production of diagnostic proteins against lymphatic filariasis, a neglected tropical infectious disease which has a negative impact on socioeconomic development. This is the first report of the integration, expression and efficacy of a diagnostic candidate of lymphatic filariasis in plants.Key MessageTransgenic tobacco plants with WbSXP-1, a filarial diagnostic candidate, were developed. The plant-produced protein showed immunoreactivity on par with the E. coli product.
Collapse
|
96
|
Cheng F, Kardashliev T, Pitzler C, Shehzad A, Lue H, Bernhagen J, Zhu L, Schwaneberg U. A Competitive Flow Cytometry Screening System for Directed Evolution of Therapeutic Enzyme. ACS Synth Biol 2015; 4:768-75. [PMID: 25658761 DOI: 10.1021/sb500343g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A ligand-mediated eGFP-expression system (LiMEx) was developed as a novel flow cytometry based screening platform that relies on a competitive conversion/binding of arginine between arginine deiminase and arginine repressor. Unlike product-driven detection systems, the competitive screening platform allows to evolve enzymes toward efficient operation at low substrate concentrations under physiological conditions. The principle of LiMEx was validated by evolving arginine deiminase (ADI, an anticancer therapeutic) for stronger inhibition of tumor growth. After screening of ∼8.2 × 10(6) clones in three iterative rounds of epPCR libraries, PpADI (ADI from Pseudomonas plecoglossicida) variant M31 with reduced S0.5 value (0.17 mM compared to 1.23 mM (WT)) and, importantly, increased activity at physiological arginine concentration (M31:6.14 s(-1); WT: not detectable) was identified. Moreover, M31 showed a significant inhibitory effect against SK-MEL-28 and G361 melanoma cell lines. (IC50 = 0.02 μg/mL for SK-MEL-28 and G361).
Collapse
Affiliation(s)
- Feng Cheng
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Tsvetan Kardashliev
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Christian Pitzler
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Aamir Shehzad
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Hongqi Lue
- Institute
of Biochemistry and Molecular Cell Biology, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Jürgen Bernhagen
- Institute
of Biochemistry and Molecular Cell Biology, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Leilei Zhu
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| |
Collapse
|
97
|
Goyal M, Chaudhuri TK. GroEL–GroES assisted folding of multiple recombinant proteins simultaneously over-expressed in Escherichia coli. Int J Biochem Cell Biol 2015; 64:277-86. [DOI: 10.1016/j.biocel.2015.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/17/2015] [Accepted: 04/28/2015] [Indexed: 11/16/2022]
|
98
|
Kumar S, Jain KK, Singh A, Panda AK, Kuhad RC. Characterization of recombinant pectate lyase refolded from inclusion bodies generated in E. coli BL21(DE3). Protein Expr Purif 2015; 110:43-51. [DOI: 10.1016/j.pep.2014.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/03/2014] [Accepted: 12/04/2014] [Indexed: 11/15/2022]
|
99
|
Zorman S, Botte M, Jiang Q, Collinson I, Schaffitzel C. Advances and challenges of membrane–protein complex production. Curr Opin Struct Biol 2015; 32:123-30. [DOI: 10.1016/j.sbi.2015.03.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/24/2015] [Accepted: 03/26/2015] [Indexed: 01/14/2023]
|
100
|
Bayer T, Milker S, Wiesinger T, Rudroff F, Mihovilovic MD. Designer Microorganisms for Optimized Redox Cascade Reactions - Challenges and Future Perspectives. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|