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Chavez D, Amarquaye GN, Mejia-Santana A, Dyotima, Ryan K, Zeng L, Landeta C. Warfarin analogs target disulfide bond-forming enzymes and suggest a residue important for quinone and coumarin binding. J Biol Chem 2024; 300:107383. [PMID: 38762182 PMCID: PMC11208910 DOI: 10.1016/j.jbc.2024.107383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024] Open
Abstract
Disulfide bond formation has a central role in protein folding of both eukaryotes and prokaryotes. In bacteria, disulfide bonds are catalyzed by DsbA and DsbB/VKOR enzymes. First, DsbA, a periplasmic disulfide oxidoreductase, introduces disulfide bonds into substrate proteins. Then, the membrane enzyme, either DsbB or VKOR, regenerate DsbA's activity by the formation of de novo disulfide bonds which reduce quinone. We have previously performed a high-throughput chemical screen and identified a family of warfarin analogs that target either bacterial DsbB or VKOR. In this work, we expressed functional human VKORc1 in Escherichia coli and performed a structure-activity-relationship analysis to study drug selectivity between bacterial and mammalian enzymes. We found that human VKORc1 can function in E. coli by removing two positive residues, allowing the search for novel anticoagulants using bacteria. We also found one warfarin analog capable of inhibiting both bacterial DsbB and VKOR and a second one antagonized only the mammalian enzymes when expressed in E. coli. The difference in the warfarin structure suggests that substituents at positions three and six in the coumarin ring can provide selectivity between the bacterial and mammalian enzymes. Finally, we identified the two amino acid residues responsible for drug binding. One of these is also essential for de novo disulfide bond formation in both DsbB and VKOR enzymes. Our studies highlight a conserved role of this residue in de novo disulfide-generating enzymes and enable the design of novel anticoagulants or antibacterials using coumarin as a scaffold.
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Affiliation(s)
- Dariana Chavez
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | | | - Dyotima
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Kayley Ryan
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Lifan Zeng
- Department of Biochemistry and Molecular Biology, Indiana University Chemical Genomics Core Facility, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Cristina Landeta
- Department of Biology, Indiana University, Bloomington, Indiana, USA.
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2
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Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more suitable for specific applications. Since the first in vitro evolution experiments performed by Sol Spiegelman in 1967, a wide range of techniques have been developed to tackle the main two steps of directed evolution: genetic diversification (library generation), and isolation of the variants of interest. This review covers the main modern methodologies, discussing the advantages and drawbacks of each, and hence the considerations for designing directed evolution experiments. Furthermore, the most recent developments are discussed, showing how advances in the handling of ever larger library sizes are enabling new research questions to be tackled.
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Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- School of Life Sciences, The University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
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3
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Li W. Distinct enzymatic strategies for de novo generation of disulfide bonds in membranes. Crit Rev Biochem Mol Biol 2023; 58:36-49. [PMID: 37098102 PMCID: PMC10460286 DOI: 10.1080/10409238.2023.2201404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
Disulfide bond formation is a catalyzed reaction essential for the folding and stability of proteins in the secretory pathway. In prokaryotes, disulfide bonds are generated by DsbB or VKOR homologs that couple the oxidation of a cysteine pair to quinone reduction. Vertebrate VKOR and VKOR-like enzymes have gained the epoxide reductase activity to support blood coagulation. The core structures of DsbB and VKOR variants share the architecture of a four-transmembrane-helix bundle that supports the coupled redox reaction and a flexible region containing another cysteine pair for electron transfer. Despite considerable similarities, recent high-resolution crystal structures of DsbB and VKOR variants reveal significant differences. DsbB activates the cysteine thiolate by a catalytic triad of polar residues, a reminiscent of classical cysteine/serine proteases. In contrast, bacterial VKOR homologs create a hydrophobic pocket to activate the cysteine thiolate. Vertebrate VKOR and VKOR-like maintain this hydrophobic pocket and further evolved two strong hydrogen bonds to stabilize the reaction intermediates and increase the quinone redox potential. These hydrogen bonds are critical to overcome the higher energy barrier required for epoxide reduction. The electron transfer process of DsbB and VKOR variants uses slow and fast pathways, but their relative contribution may be different in prokaryotic and eukaryotic cells. The quinone is a tightly bound cofactor in DsbB and bacterial VKOR homologs, whereas vertebrate VKOR variants use transient substrate binding to trigger the electron transfer in the slow pathway. Overall, the catalytic mechanisms of DsbB and VKOR variants have fundamental differences.
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Affiliation(s)
- Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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4
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Nwabuife JC, Omolo CA, Govender T. Nano delivery systems to the rescue of ciprofloxacin against resistant bacteria "E. coli; P. aeruginosa; Saureus; and MRSA" and their infections. J Control Release 2022; 349:338-353. [PMID: 35820538 DOI: 10.1016/j.jconrel.2022.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/29/2022] [Accepted: 07/03/2022] [Indexed: 10/17/2022]
Abstract
Ciprofloxacin (CIP) a broad-spectrum antibiotic, is used extensively for the treatment of diverse infections and diseases of bacteria origin, and this includes infections caused by E. coli; P. aeruginosa; S. aureus; and MRSA. This extensive use of CIP has therefore led to an increase in resistance by these infection causing organisms. Nano delivery systems has recently proven to be a possible solution to resistance to these organisms. They have been applied as a strategy to improve the target specificity of CIP against infections and diseases caused by these organisms, thereby maximising the efficacy of CIP to overcome the resistance. Herein, we proffer a brief overview of the mechanisms of resistance; the causes of resistance; and the various approaches employed to overcome this resistance. The review then proceeds to critically evaluate various nano delivery systems including inorganic based nanoparticles; lipid-based nanoparticles; capsules, dendrimers, hydrogels, micelles, and polymeric nanoparticles; and others; that have been applied for the delivery of CIP against E. coli; P. aeruginosa; S. aureus; and MRSA infections. Finally, the review highlights future areas of research, for the optimisation of various nano delivery systems, to maximise the therapeutic efficacy of CIP against these organisms. This review confirms the potential of nano delivery systems, for addressing the challenges of resistance to caused by E. coli; P. aeruginosa; S. aureus; and MRSA to CIP.
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Affiliation(s)
- Joshua C Nwabuife
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Calvin A Omolo
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.; Department of Pharmaceutics, School of Pharmacy and Health Sciences, United States International University-Africa, P. O. Box 14634-00800, Nairobi, Kenya
| | - Thirumala Govender
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa..
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5
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Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 2020; 9:e58026. [PMID: 32870157 PMCID: PMC7462613 DOI: 10.7554/elife.58026] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 01/05/2023] Open
Abstract
Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR's pivotal role in coagulation, its structure and active site remain poorly understood. In addition, VKOR variants can cause vitamin K-dependent clotting factor deficiency or alter warfarin response. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells. The large-scale functional data, along with an evolutionary coupling analysis, supports a four transmembrane domain topology, with variants in transmembrane domains exhibiting strongly deleterious effects on abundance and activity. Functionally constrained regions of the protein define the active site, and we find that, of four conserved cysteines putatively critical for function, only three are absolutely required. Finally, 25% of human VKOR missense variants show reduced abundance or activity, possibly conferring warfarin sensitivity or causing disease.
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Affiliation(s)
- Melissa A Chiasson
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Nathan J Rollins
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Jason J Stephany
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Katherine A Sitko
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Marta Verby
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Song Sun
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | | | - Debora S Marks
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Douglas M Fowler
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Bioengineering, University of WashingtonSeattleUnited States
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6
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Zhu DM, Li QH, Shen Y, Zhang Q. Risk factors for quinolone-resistant Escherichia coli infection: a systematic review and meta-analysis. Antimicrob Resist Infect Control 2020; 9:11. [PMID: 31938541 PMCID: PMC6953284 DOI: 10.1186/s13756-019-0675-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023] Open
Abstract
Background Antimicrobial resistance to quinolone is rising worldwide, especially in Escherichia coli causing various infections. Although many studies have been conducted to identify the risk factors for quinolone-resistant Escherichia coli (QREC) infection, the results are inconsistent and have not been systematically reported. The aim of the present study is to conduct a systematic review and meta-analysis to evaluate the potential risk factors for QREC infection. Methods A systematic search was performed to collect published data in the EMBASE, PubMed, and the Cochrane Library up to April 2019. Risk factors were analyzed using the pooled odds ratio (ORs) with 95% confidence interval (CIs). Results Twenty-seven trials involving 67,019 participants were included in the present study. The following risk factors associated with QREC infection were identified: (1) male (OR = 1.41), (2) hepatic cirrhosis (OR = 2.05), (3) diabetes mellitus (OR = 1.62), (4) cardiovascular disease (OR = 1.76), (5) neurogenic bladder (OR = 8.66), (6) renal dysfunction (OR = 2.47), (7) transplantation (OR = 2.37), (8) urinary tract infection (OR = 2.79) and urinary tract abnormality (OR = 1.85), (9) dementia (OR = 5.83), (10) heart failure (OR = 5.63), (11) neurologic disease (OR = 2.80), (12) immunosuppressive drugs (OR = 2.02), (13) urinary catheter (OR = 4.39), (14) nursing home resident (OR = 4.63), (15) prior surgery (OR = 2.54), (16) quinolones (OR = 7.67), (17) other antibiotics (OR = 2.74), (18) hospitalization (OR = 2.06) and (19) nosocomial infection acquisition (OR = 2.35). Conclusions QREC infection was associated with nineteen risk factors including prior quinolones use, hospitalization, and several comorbidities. Reducing exposure to these risk factors and modification of antibiotic use are important to prevent quinolone resistance.
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Affiliation(s)
- Dong-Mei Zhu
- Department of Hospital Infection Control, Chongqing Health Center for Women and Children, 120 Longshan Road, Chongqing, Chongqing, 400013 China
| | - Qiu-Hong Li
- Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, Chongqing, 400013 China
| | - Yan Shen
- Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, Chongqing, 400013 China
| | - Qin Zhang
- Department of Hospital Infection Control, Chongqing Health Center for Women and Children, 120 Longshan Road, Chongqing, Chongqing, 400013 China
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7
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Steinberg R, Knüpffer L, Origi A, Asti R, Koch HG. Co-translational protein targeting in bacteria. FEMS Microbiol Lett 2019; 365:4966980. [PMID: 29790984 DOI: 10.1093/femsle/fny095] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/09/2018] [Indexed: 01/16/2023] Open
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and have to be transported into or across the cytoplasmic membrane. Bacteria use multiple protein transport systems in parallel, but the majority of proteins engage two distinct targeting systems. One is the co-translational targeting by two universally conserved GTPases, the signal recognition particle (SRP) and its receptor FtsY, which deliver inner membrane proteins to either the SecYEG translocon or the YidC insertase for membrane insertion. The other targeting system depends on the ATPase SecA, which targets secretory proteins, i.e. periplasmic and outer membrane proteins, to SecYEG for their subsequent ATP-dependent translocation. While SRP selects its substrates already very early during their synthesis, the recognition of secretory proteins by SecA is believed to occur primarily after translation termination, i.e. post-translationally. In this review we highlight recent progress on how SRP recognizes its substrates at the ribosome and how the fidelity of the targeting reaction to SecYEG is maintained. We furthermore discuss similarities and differences in the SRP-dependent targeting to either SecYEG or YidC and summarize recent results that suggest that some membrane proteins are co-translationally targeted by SecA.
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Affiliation(s)
- Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Lara Knüpffer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, Freiburg D-79104, Germany
| | - Rossella Asti
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
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8
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Landeta C, McPartland L, Tran NQ, Meehan BM, Zhang Y, Tanweer Z, Wakabayashi S, Rock J, Kim T, Balasubramanian D, Audette R, Toosky M, Pinkham J, Rubin EJ, Lory S, Pier G, Boyd D, Beckwith J. Inhibition of Pseudomonas aeruginosa and Mycobacterium tuberculosis disulfide bond forming enzymes. Mol Microbiol 2019; 111:918-937. [PMID: 30556355 DOI: 10.1111/mmi.14185] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2018] [Indexed: 01/16/2023]
Abstract
In bacteria, disulfide bonds confer stability on many proteins exported to the cell envelope or beyond, including bacterial virulence factors. Thus, proteins involved in disulfide bond formation represent good targets for the development of inhibitors that can act as antibiotics or anti-virulence agents, resulting in the simultaneous inactivation of several types of virulence factors. Here, we present evidence that the disulfide bond forming enzymes, DsbB and VKOR, are required for Pseudomonas aeruginosa pathogenicity and Mycobacterium tuberculosis survival respectively. We also report the results of a HTS of 216,767 compounds tested against P. aeruginosa DsbB1 and M. tuberculosis VKOR using Escherichia coli cells. Since both P. aeruginosa DsbB1 and M. tuberculosis VKOR complement an E. coli dsbB knockout, we screened simultaneously for inhibitors of each complemented E. coli strain expressing a disulfide-bond sensitive β-galactosidase reported previously. The properties of several inhibitors obtained from these screens suggest they are a starting point for chemical modifications with potential for future antibacterial development.
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Affiliation(s)
- Cristina Landeta
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Laura McPartland
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Ngoc Q Tran
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Brian M Meehan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Yifan Zhang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Zaidi Tanweer
- Division of Infectious Diseases. Department of Medicine. Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shoko Wakabayashi
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Jeremy Rock
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Taehyun Kim
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | | | - Rebecca Audette
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Melody Toosky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Jessica Pinkham
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Stephen Lory
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Gerald Pier
- Division of Infectious Diseases. Department of Medicine. Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dana Boyd
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Jon Beckwith
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
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9
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Karyolaimos A, Ampah-Korsah H, Zhang Z, de Gier JW. Shaping Escherichia coli for recombinant membrane protein production. FEMS Microbiol Lett 2018; 365:5040224. [DOI: 10.1093/femsle/fny152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/18/2018] [Indexed: 12/29/2022] Open
Affiliation(s)
- Alexandros Karyolaimos
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Henry Ampah-Korsah
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Zhe Zhang
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
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10
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Hibender S, Landeta C, Berkmen M, Beckwith J, Boyd D. Aeropyrum pernix membrane topology of protein VKOR promotes protein disulfide bond formation in two subcellular compartments. MICROBIOLOGY-SGM 2017; 163:1864-1879. [PMID: 29139344 DOI: 10.1099/mic.0.000569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Disulfide bonds confer stability and activity to proteins. Bioinformatic approaches allow predictions of which organisms make protein disulfide bonds and in which subcellular compartments disulfide bond formation takes place. Such an analysis, along with biochemical and protein structural data, suggests that many of the extremophile Crenarachaea make protein disulfide bonds in both the cytoplasm and the cell envelope. We have sought to determine the oxidative folding pathways in the sequenced genomes of the Crenarchaea, by seeking homologues of the enzymes known to be involved in disulfide bond formation in bacteria. Some Crenarchaea have two homologues of the cytoplasmic membrane protein VKOR, a protein required in many bacteria for the oxidation of bacterial DsbAs. We show that the two VKORs of Aeropyrum pernix assume opposite orientations in the cytoplasmic membrane, when expressed in E. coli. One has its active cysteines oriented toward the E. coli periplasm (ApVKORo) and the other toward the cytoplasm (ApVKORi). Furthermore, the ApVKORo promotes disulfide bond formation in the E. coli cell envelope, while the ApVKORi promotes disulfide bond formation in the E. coli cytoplasm via a co-expressed archaeal protein ApPDO. Amongst the VKORs from different archaeal species, the pairs of VKORs in each species are much more closely related to each other than to the VKORs of the other species. The results suggest two independent occurrences of the evolution of the two topologically inverted VKORs in archaea. Our results suggest a mechanistic basis for the formation of disulfide bonds in the cytoplasm of Crenarchaea.
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Affiliation(s)
- Stijntje Hibender
- Faculty of Science, University of Amsterdam, Postbus 94216, 1090 GE Amsterdam, The Netherlands
| | - Cristina Landeta
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jon Beckwith
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Dana Boyd
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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11
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Konczal J, Gray CH. Streamlining workflow and automation to accelerate laboratory scale protein production. Protein Expr Purif 2017; 133:160-169. [PMID: 28330825 DOI: 10.1016/j.pep.2017.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/17/2017] [Indexed: 12/20/2022]
Abstract
Protein production facilities are often required to produce diverse arrays of proteins for demanding methodologies including crystallography, NMR, ITC and other reagent intensive techniques. It is common for these teams to find themselves a bottleneck in the pipeline of ambitious projects. This pressure to deliver has resulted in the evolution of many novel methods to increase capacity and throughput at all stages in the pipeline for generation of recombinant proteins. This review aims to describe current and emerging options to accelerate the success of protein production in Escherichia coli. We emphasize technologies that have been evaluated and implemented in our laboratory, including innovative molecular biology and expression vectors, small-scale expression screening strategies and the automation of parallel and multidimensional chromatography.
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Affiliation(s)
- Jennifer Konczal
- Drug Discovery Program, CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom
| | - Christopher H Gray
- Drug Discovery Program, CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom.
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12
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Schlegel S, Genevaux P, de Gier JW. Isolating Escherichia coli strains for recombinant protein production. Cell Mol Life Sci 2016; 74:891-908. [PMID: 27730255 PMCID: PMC5306230 DOI: 10.1007/s00018-016-2371-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/22/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Escherichia coli has been widely used for the production of recombinant proteins. To improve protein production yields in E. coli, directed engineering approaches have been commonly used. However, there are only few reported examples of the isolation of E. coli protein production strains using evolutionary approaches. Here, we first give an introduction to bacterial evolution and mutagenesis to set the stage for discussing how so far selection- and screening-based approaches have been used to isolate E. coli protein production strains. Finally, we discuss how evolutionary approaches may be used in the future to isolate E. coli strains with improved protein production characteristics.
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Affiliation(s)
- Susan Schlegel
- Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusväg 16C, 106 91, Stockholm, Sweden.
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