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Tan YJ, Abdelkader EH, Tarcoveanu E, Maleckis A, Nitsche C, Otting G. (2 S,4 S)-5-Fluoroleucine, (2 S,4 R)-5-Fluoroleucine, and 5,5'-Difluoroleucine in Escherichia coli PpiB: Protein Production, 19F NMR, and Ligand Sensing Enhanced by the γ-Gauche Effect. Biochemistry 2024; 63:1376-1387. [PMID: 38753308 DOI: 10.1021/acs.biochem.4c00080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Global substitution of leucine for analogues containing CH2F instead of methyl groups delivers proteins with multiple sites for monitoring by 19F nuclear magnetic resonance (NMR) spectroscopy. The 19 kDa Escherichia coli peptidyl-prolyl cis-trans isomerase B (PpiB) was prepared with uniform high-level substitution of leucine by (2S,4S)-5-fluoroleucine, (2S,4R)-5-fluoroleucine, or 5,5'-difluoroleucine. The stability of the samples toward thermal denaturation was little altered compared to the wild-type protein. 19F nuclear magnetic resonance (NMR) spectra showed large chemical shift dispersions between 6 and 17 ppm. The 19F chemical shifts correlate with the three-bond 1H-19F couplings (3JHF), providing the first experimental verification of the γ-gauche effect predicted by [Feeney, J. J. Am. Chem. Soc. 1996, 118, 8700-8706] and establishing the effect as the predominant determinant of the 19F chemical shifts of CH2F groups. Individual CH2F groups can be confined to single rotameric states by the protein environment, but most CH2F groups exchange between different rotamers at a rate that is fast on the NMR chemical shift scale. Interactions between fluorine atoms in 5,5'-difluoroleucine bias the CH2F rotamers in agreement with results obtained previously for 1,3-difluoropropane. The sensitivity of the 19F chemical shift to the rotameric state of the CH2F groups potentially renders them particularly sensitive for detecting allosteric effects.
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Affiliation(s)
- Yi Jiun Tan
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Eliza Tarcoveanu
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Ansis Maleckis
- Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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2
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Maxwell M, Tan YJ, Lee R, Huber T, Otting G. Electrostatic Contribution to 19F Chemical Shifts in Fluorotryptophans in Proteins. Biochemistry 2023; 62:3255-3264. [PMID: 37934875 DOI: 10.1021/acs.biochem.3c00408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
DFT calculations indicate that the 19F chemical shifts of aromatic rings containing single fluorine substituents are sensitive to the electric fields and electric field gradients at the position of the fluorine atom. The present work explores whether long-range structure restraints can be gained from changes in 19F chemical shifts following mutations of charged to uncharged residues. 19F chemical shifts of fluorotryptophan residues were measured in two different proteins, GB1 and the NT* domain, following mutations of single asparagine residues to aspartic acid. Four different versions of fluorotryptophan were investigated, including 4-, 5-, 6-, and 7-fluorotryptophan, which were simultaneously installed by cell-free protein synthesis using 4-, 5-, 6-, and 7-fluoroindole as precursors for the tryptophan synthase present in the S30 extract. For comparison, the 1H chemical shifts of the corresponding nonfluorinated protein mutants produced with 13C-labeled tryptophan were also measured. The results show that the 19F chemical shifts respond more sensitively to the charge mutations than the 1H chemical shifts in the nonfluorinated references, but the chemical shift changes were much smaller than predicted by DFT calculations of fluoroindoles in the electric field of a partial charge in vacuum, indicating comprehensive dielectric shielding by water and protein. No straightforward correlation with the location of the charge mutation could be established.
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Affiliation(s)
- Michael Maxwell
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Yi Jiun Tan
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Richmond Lee
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong 2500, New South Wales, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Gottfried Otting
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
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3
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Goodall DJ, Warecka D, Hawkins M, Rudolph CJ. Interplay between chromosomal architecture and termination of DNA replication in bacteria. Front Microbiol 2023; 14:1180848. [PMID: 37434703 PMCID: PMC10331603 DOI: 10.3389/fmicb.2023.1180848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Faithful transmission of the genome from one generation to the next is key to life in all cellular organisms. In the majority of bacteria, the genome is comprised of a single circular chromosome that is normally replicated from a single origin, though additional genetic information may be encoded within much smaller extrachromosomal elements called plasmids. By contrast, the genome of a eukaryote is distributed across multiple linear chromosomes, each of which is replicated from multiple origins. The genomes of archaeal species are circular, but are predominantly replicated from multiple origins. In all three cases, replication is bidirectional and terminates when converging replication fork complexes merge and 'fuse' as replication of the chromosomal DNA is completed. While the mechanics of replication initiation are quite well understood, exactly what happens during termination is far from clear, although studies in bacterial and eukaryotic models over recent years have started to provide some insight. Bacterial models with a circular chromosome and a single bidirectional origin offer the distinct advantage that there is normally just one fusion event between two replication fork complexes as synthesis terminates. Moreover, whereas termination of replication appears to happen in many bacteria wherever forks happen to meet, termination in some bacterial species, including the well-studied bacteria Escherichia coli and Bacillus subtilis, is more restrictive and confined to a 'replication fork trap' region, making termination even more tractable. This region is defined by multiple genomic terminator (ter) sites, which, if bound by specific terminator proteins, form unidirectional fork barriers. In this review we discuss a range of experimental results highlighting how the fork fusion process can trigger significant pathologies that interfere with the successful conclusion of DNA replication, how these pathologies might be resolved in bacteria without a fork trap system and how the acquisition of a fork trap might have provided an alternative and cleaner solution, thus explaining why in bacterial species that have acquired a fork trap system, this system is remarkably well maintained. Finally, we consider how eukaryotic cells can cope with a much-increased number of termination events.
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Affiliation(s)
- Daniel J. Goodall
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | | | | | - Christian J. Rudolph
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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Mekkattu Tharayil S, Mahawaththa MC, Feintuch A, Maleckis A, Ullrich S, Morewood R, Maxwell MJ, Huber T, Nitsche C, Goldfarb D, Otting G. Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:169-182. [PMID: 37904871 PMCID: PMC10539774 DOI: 10.5194/mr-3-169-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 11/01/2023]
Abstract
The paramagnetism of a lanthanoid tag site-specifically installed on a protein provides a rich source of structural information accessible by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy. Here we report a lanthanoid tag for selective reaction with cysteine or selenocysteine with formation of a (seleno)thioether bond and a short tether between the lanthanoid ion and the protein backbone. The tag is assembled on the protein in three steps, comprising (i) reaction with 4-fluoro-2,6-dicyanopyridine (FDCP); (ii) reaction of the cyano groups with α -cysteine, penicillamine or β -cysteine to complete the lanthanoid chelating moiety; and (iii) titration with a lanthanoid ion. FDCP reacts much faster with selenocysteine than cysteine, opening a route for selective tagging in the presence of solvent-exposed cysteine residues. Loaded with Tb 3 + and Tm 3 + ions, pseudocontact shifts were observed in protein NMR spectra, confirming that the tag delivers good immobilisation of the lanthanoid ion relative to the protein, which was also manifested in residual dipolar couplings. Completion of the tag with different 1,2-aminothiol compounds resulted in different magnetic susceptibility tensors. In addition, the tag proved suitable for measuring distance distributions in double electron-electron resonance experiments after titration with Gd 3 + ions.
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Affiliation(s)
| | - Mithun C. Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michael J. Maxwell
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Escherichia coli cell factories with altered chromosomal replication scenarios exhibit accelerated growth and rapid biomass production. Microb Cell Fact 2022; 21:125. [PMID: 35729580 PMCID: PMC9210752 DOI: 10.1186/s12934-022-01851-z] [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: 04/03/2022] [Accepted: 05/21/2022] [Indexed: 11/24/2022] Open
Abstract
Background Generally, bacteria have a circular genome with a single replication origin for each replicon, whereas archaea and eukaryotes can have multiple replication origins in a single chromosome. In Escherichia coli, bidirectional DNA replication is initiated at the origin of replication (oriC) and arrested by the 10 termination sites (terA–J). Results We constructed E. coli derivatives with additional or ectopic replication origins, which demonstrate the relationship between DNA replication and cell physiology. The cultures of E. coli derivatives with multiple replication origins contained an increased fraction of replicating chromosomes and the cells varied in size. Without the original oriC, E. coli derivatives with double ectopic replication origins manifested impaired growth irrespective of growth conditions and enhanced cell size, and exhibited excessive and asynchronous replication initiation. The generation time of an E. coli strain with three replication origins decreased in a minimal medium supplemented with glucose as the sole carbon source. As well as cell growth, the introduction of additional replication origins promoted increased biomass production. Conclusions Balanced cell growth and physiological stability of E. coli under rapid growth condition are affected by changes in the position and number of replication origins. Additionally, we show that, for the first time to our knowledge, the introduction of replication initiation sites to the chromosome promotes cell growth and increases protein production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01851-z.
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Jash C, Feintuch A, Nudelman S, Manukovsky N, Abdelkader EH, Bhattacharya S, Jeschke G, Otting G, Goldfarb D. DEER experiments reveal fundamental differences between calmodulin complexes with IQ and MARCKS peptides in solution. Structure 2022; 30:813-827.e5. [PMID: 35397204 DOI: 10.1016/j.str.2022.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]
Abstract
Calmodulin (CaM) is a calcium-binding protein that regulates the function of many proteins by indirectly conferring Ca2+ sensitivity, and it undergoes a large conformational change on partners' binding. We compared the solution binding mode of the target peptides MARCKS and IQ by double electron-electron resonance (DEER) distance measurements and paramagnetic NMR. We combined nitroxide and Gd(III) spin labels, including specific substitution of one of the Ca2+ ions in the CaM mutant N60D by a Gd(III) ion. The binding of MARCKS to holo-CaM resulted neither in a closed conformation nor in a unique relative orientation between the two CaM domains, in contrast with the crystal structure. Binding of IQ to holo-CaM did generate a closed conformation. Using elastic network modeling and 12 distance restraints obtained from multiple holo-CaM/IQ DEER data, we derived a model of the solution structure, which is in reasonable agreement with the crystal structure.
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Affiliation(s)
- Chandrima Jash
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Nudelman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Nurit Manukovsky
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Sudeshna Bhattacharya
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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7
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Toft CJ, Moreau MJJ, Perutka J, Mandapati S, Enyeart P, Sorenson AE, Ellington AD, Schaeffer PM. Delineation of the Ancestral Tus-Dependent Replication Fork Trap. Int J Mol Sci 2021; 22:ijms222413533. [PMID: 34948327 PMCID: PMC8707476 DOI: 10.3390/ijms222413533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 12/28/2022] Open
Abstract
In Escherichia coli, DNA replication termination is orchestrated by two clusters of Ter sites forming a DNA replication fork trap when bound by Tus proteins. The formation of a ‘locked’ Tus–Ter complex is essential for halting incoming DNA replication forks. However, the absence of replication fork arrest at some Ter sites raised questions about their significance. In this study, we examined the genome-wide distribution of Tus and found that only the six innermost Ter sites (TerA–E and G) were significantly bound by Tus. We also found that a single ectopic insertion of TerB in its non-permissive orientation could not be achieved, advocating against a need for ‘back-up’ Ter sites. Finally, examination of the genomes of a variety of Enterobacterales revealed a new replication fork trap architecture mostly found outside the Enterobacteriaceae family. Taken together, our data enabled the delineation of a narrow ancestral Tus-dependent DNA replication fork trap consisting of only two Ter sites.
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Affiliation(s)
- Casey J. Toft
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia; (C.J.T.); (M.J.J.M.); (A.E.S.)
- Centre of Tropical Bioinformatics and Molecular Biology, James Cook University, Douglas, QLD 4811, Australia
| | - Morgane J. J. Moreau
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia; (C.J.T.); (M.J.J.M.); (A.E.S.)
| | - Jiri Perutka
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; (J.P.); (S.M.); (P.E.); (A.D.E.)
| | - Savitri Mandapati
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; (J.P.); (S.M.); (P.E.); (A.D.E.)
| | - Peter Enyeart
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; (J.P.); (S.M.); (P.E.); (A.D.E.)
| | - Alanna E. Sorenson
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia; (C.J.T.); (M.J.J.M.); (A.E.S.)
| | - Andrew D. Ellington
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; (J.P.); (S.M.); (P.E.); (A.D.E.)
| | - Patrick M. Schaeffer
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia; (C.J.T.); (M.J.J.M.); (A.E.S.)
- Centre of Tropical Bioinformatics and Molecular Biology, James Cook University, Douglas, QLD 4811, Australia
- Correspondence: ; Tel.: +61-(0)-7-4781-4448; Fax: +61-(0)-7-4781-6078
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8
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Maleckis A, Herath ID, Otting G. Synthesis of 13C/ 19F/ 2H labeled indoles for use as tryptophan precursors for protein NMR spectroscopy. Org Biomol Chem 2021; 19:5133-5147. [PMID: 34032255 DOI: 10.1039/d1ob00611h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Synthesis of indoles labeled with 13C-1H and 13C-19F spin pairs is described. All syntheses utilize inexpensive carbon-13C dioxide as the 13C isotope source. Ruthenium-mediated ring-closing metathesis is the key step in construction of the 13C containing indole carbocycle. Fluorine is introduced via electrophilic fluorination at the 7-position and via palladium-mediated cross-coupling at the 4-position. Indole and fluoroindoles are viable tryptophan precursors for in vivo protein expression. We show that they are viable also in in vitro protein synthesis using standard E. coli S30 extracts. Incorporation of the synthesized 13C-1H and 13C-19F spin pair labeled tryptophans into proteins enables high-resolution and high-sensitivity nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
| | - Iresha D Herath
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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9
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Siddiquee R, Kwan AH. Cell-free Synthesis of Correctly Folded Proteins with Multiple Disulphide Bonds: Production of Fungal Hydrophobins. Bio Protoc 2021; 11:e4019. [PMID: 34150926 DOI: 10.21769/bioprotoc.4019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 11/02/2022] Open
Abstract
Cell-free synthesis is a powerful technique that uses the transcriptional and translational machinery extracted from cells to create proteins without the constraints of living cells. Here, we report a cell-free protein production protocol using Escherichia coli lysate (Figure 1) to successfully express a class of proteins (known as hydrophobins) with multiple intramolecular disulphide bonds which are typically difficult to express in a soluble and folded state in the reducing environments found inside a cell. In some cases, the inclusion of a recombinant disulphide isomerase DsbC further enhances the expression levels of correctly folded hydrophobins. Using this protocol, we can achieve milligram levels of protein expression per ml of reaction. While our target proteins are the fungal hydrophobins, it is likely that this protocol with some minor variations can be used to express other proteins with multiple intramolecular disulphide bonds in a natively folded state. Graphic abstract: Figure 1.Workflow for cell-free protein expression and single-step purification using affinity chromatography. A. E. coli S30 lysate prepared as described in Apponyi et al. (2008) can be stored for up to several years at -80°C without any loss of activity in our experience. B. The S30 lysate, plasmid DNA that encodes for the protein of interest along with an affinity tag and components required for transcription and translation are added to the reaction mix. Following a single-step protein purification, the protein of interest can be isolated for further use.
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Affiliation(s)
- Rezwan Siddiquee
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia.,The University of Sydney Nano Institute, University of Sydney, NSW, Australia
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10
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Welegedara AP, Maleckis A, Bandara R, Mahawaththa MC, Dilhani Herath I, Jiun Tan Y, Giannoulis A, Goldfarb D, Otting G, Huber T. Cell-Free Synthesis of Selenoproteins in High Yield and Purity for Selective Protein Tagging. Chembiochem 2021; 22:1480-1486. [PMID: 33319405 DOI: 10.1002/cbic.202000785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Indexed: 01/10/2023]
Abstract
The selenol group of selenocysteine is much more nucleophilic than the thiol group of cysteine. Selenocysteine residues in proteins thus offer reactive points for rapid post-translational modification. Herein, we show that selenoproteins can be expressed in high yield and purity by cell-free protein synthesis by global substitution of cysteine by selenocysteine. Complete alkylation of solvent-exposed selenocysteine residues was achieved in 10 minutes with 4-chloromethylene dipicolinic acid (4Cl-MDPA) under conditions that left cysteine residues unchanged even after overnight incubation. GdIII -GdIII distances measured by double electron-electron resonance (DEER) experiments of maltose binding protein (MBP) containing two selenocysteine residues tagged with 4Cl-MDPA-GdIII were indistinguishable from GdIII -GdIII distances measured of MBP containing cysteine reacted with 4Br-MDPA tags.
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Affiliation(s)
- Adarshi P Welegedara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.,Department of Chemistry, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, 1006, Riga, Latvia
| | - Ruchira Bandara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Mithun C Mahawaththa
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Iresha Dilhani Herath
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Yi Jiun Tan
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Angeliki Giannoulis
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
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11
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Mekkattu Tharayil S, Mahawaththa M, Loh CT, Adekoya I, Otting G. Phosphoserine for the generation of lanthanide-binding sites on proteins for paramagnetic nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:1-13. [PMID: 37904776 PMCID: PMC10539748 DOI: 10.5194/mr-2-1-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/12/2020] [Indexed: 11/01/2023]
Abstract
Pseudocontact shifts (PCSs) generated by paramagnetic lanthanide ions provide valuable long-range structural information in nuclear magnetic resonance (NMR) spectroscopic analyses of biological macromolecules such as proteins, but labelling proteins site-specifically with a single lanthanide ion remains an ongoing challenge, especially for proteins that are not suitable for ligation with cysteine-reactive lanthanide complexes. We show that a specific lanthanide-binding site can be installed on proteins by incorporation of phosphoserine in conjunction with other negatively charged residues, such as aspartate, glutamate or a second phosphoserine residue. The close proximity of the binding sites to the protein backbone leads to good immobilization of the lanthanide ion, as evidenced by the excellent quality of fits between experimental PCSs and PCSs calculated with a single magnetic susceptibility anisotropy (Δ χ ) tensor. An improved two-plasmid system was designed to enhance the yields of proteins with genetically encoded phosphoserine, and good lanthanide ion affinities were obtained when the side chains of the phosphoserine and aspartate residues are not engaged in salt bridges, although the presence of too many negatively charged residues in close proximity can also lead to unfolding of the protein. In view of the quality of the Δ χ tensors that can be obtained from lanthanide-binding sites generated by site-specific incorporation of phosphoserine, this method presents an attractive tool for generating PCSs in stable proteins, particularly as it is independent of cysteine residues.
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Affiliation(s)
- Sreelakshmi Mekkattu Tharayil
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Mithun Chamikara Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Choy-Theng Loh
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
- present address: Hangzhou Wayland Bioscience Co. Ltd, Hangzhou
310030, PR China
| | - Ibidolapo Adekoya
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
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12
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Kaczmarski JA, Mahawaththa MC, Feintuch A, Clifton BE, Adams LA, Goldfarb D, Otting G, Jackson CJ. Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme. Nat Commun 2020; 11:5945. [PMID: 33230119 PMCID: PMC7683729 DOI: 10.1038/s41467-020-19695-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Several enzymes are known to have evolved from non-catalytic proteins such as solute-binding proteins (SBPs). Although attention has been focused on how a binding site can evolve to become catalytic, an equally important question is: how do the structural dynamics of a binding protein change as it becomes an efficient enzyme? Here we performed a variety of experiments, including propargyl-DO3A-Gd(III) tagging and double electron-electron resonance (DEER) to study the rigid body protein dynamics of reconstructed evolutionary intermediates to determine how the conformational sampling of a protein changes along an evolutionary trajectory linking an arginine SBP to a cyclohexadienyl dehydratase (CDT). We observed that primitive dehydratases predominantly populate catalytically unproductive conformations that are vestiges of their ancestral SBP function. Non-productive conformational states, including a wide-open state, are frozen out of the conformational landscape via remote mutations, eventually leading to extant CDT that exclusively samples catalytically relevant compact states. These results show that remote mutations can reshape the global conformational landscape of an enzyme as a mechanism for increasing catalytic activity.
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Affiliation(s)
- Joe A Kaczmarski
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Mithun C Mahawaththa
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ben E Clifton
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia.,Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0412, Japan
| | - Luke A Adams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Gottfried Otting
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, 2601, ACT, Australia.
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, 2601, ACT, Australia. .,Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, 2601, ACT, Australia.
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13
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Monachino E, Jergic S, Lewis JS, Xu ZQ, Lo ATY, O'Shea VL, Berger JM, Dixon NE, van Oijen AM. A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome. Mol Cell 2020; 79:140-154.e7. [PMID: 32464091 DOI: 10.1016/j.molcel.2020.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/12/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Recent studies of bacterial DNA replication have led to a picture of the replisome as an entity that freely exchanges DNA polymerases and displays intermittent coupling between the helicase and polymerase(s). Challenging the textbook model of the polymerase holoenzyme acting as a stable complex coordinating the replisome, these observations suggest a role of the helicase as the central organizing hub. We show here that the molecular origin of this newly found plasticity lies in the 500-fold increase in strength of the interaction between the polymerase holoenzyme and the replicative helicase upon association of the primase with the replisome. By combining in vitro ensemble-averaged and single-molecule assays, we demonstrate that this conformational switch operates during replication and promotes recruitment of multiple holoenzymes at the fork. Our observations provide a molecular mechanism for polymerase exchange and offer a revised model for the replication reaction that emphasizes its stochasticity.
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Affiliation(s)
- Enrico Monachino
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747, the Netherlands
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Allen T Y Lo
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Valerie L O'Shea
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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14
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Oxidative Catabolism of (+)-Pinoresinol Is Initiated by an Unusual Flavocytochrome Encoded by Translationally Coupled Genes within a Cluster of (+)-Pinoresinol-Coinduced Genes in Pseudomonas sp. Strain SG-MS2. Appl Environ Microbiol 2020; 86:AEM.00375-20. [PMID: 32198167 DOI: 10.1128/aem.00375-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/12/2020] [Indexed: 12/19/2022] Open
Abstract
Burkholderia sp. strain SG-MS1 and Pseudomonas sp. strain SG-MS2 have previously been found to mineralize (+)-pinoresinol through a common catabolic pathway. Here, we used comparative genomics, proteomics, protein semipurification, and heterologous expression to identify a flavoprotein from the vanillyl alcohol oxidase/p-cresol methyl hydroxylase (VAO/PCMH) enzyme family in SG-MS2 that carries out the initial hydroxylation of (+)-pinoresinol at the benzylic carbon. The cognate gene is translationally coupled with a downstream cytochrome gene, and the cytochrome is required for activity. The flavoprotein has a unique combination of cofactor binding and cytochrome requirements for the VAO/PCMH family. The heterologously expressed enzyme has a Km of 1.17 μM for (+)-pinoresinol. The enzyme is overexpressed in strain SG-MS2 upon exposure to (+)-pinoresinol, along with 45 other proteins, 22 of which were found to be encoded by genes in an approximately 35.1-kb cluster also containing the flavoprotein and cytochrome genes. Homologs of 18 of these 22 genes, plus the flavoprotein and cytochrome genes, were also found in a 38.7-kb cluster in SG-MS1. The amino acid identities of four of the other proteins within the SG-MS2 cluster suggest they catalyze conversion of hydroxylated pinoresinol to protocatechuate and 2-methoxyhydroquinone. Nine other proteins upregulated in SG-MS2 on exposure to (+)-pinoresinol appear to be homologs of proteins known to comprise the protocatechuate and 2-methoxyhydroquinone catabolic pathways, but only three of the cognate genes lie within the cluster containing the flavoprotein and cytochrome genes.IMPORTANCE (+)-Pinoresinol is an important plant defense compound, a major food lignan for humans and some other animals, and the model compound used to study degradation of the β-β' linkages in lignin. We report a gene cluster, in one strain each of Pseudomonas and Burkholderia, that is involved in the oxidative catabolism of (+)-pinoresinol. The flavoprotein component of the α-hydroxylase which heads the pathway belongs to the 4-phenol oxidizing (4PO) subgroup of the vanillyl alcohol oxidase/p-cresol methyl hydroxylase (VAO/PCMH) enzyme family but constitutes a novel combination of cofactor and electron acceptor properties for the family. It is translationally coupled with a cytochrome gene whose product is also required for activity. The work casts new light on the biology of (+)-pinoresinol and its transformation to other bioactive molecules. Potential applications of the findings include new options for deconstructing lignin into useful chemicals and the generation of new phytoestrogenic enterolactones from lignans.
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15
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Bottomley AL, Peterson E, Iosifidis G, Yong AMH, Hartley-Tassell LE, Ansari S, McKenzie C, Burke C, Duggin IG, Kline KA, Harry EJ. The novel E. coli cell division protein, YtfB, plays a role in eukaryotic cell adhesion. Sci Rep 2020; 10:6745. [PMID: 32317661 PMCID: PMC7174318 DOI: 10.1038/s41598-020-63729-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/01/2020] [Indexed: 01/10/2023] Open
Abstract
Characterisation of protein function based solely on homology searches may overlook functions under specific environmental conditions, or the possibility of a protein having multiple roles. In this study we investigated the role of YtfB, a protein originally identified in a genome-wide screen to cause inhibition of cell division, and has demonstrated to localise to the Escherichia coli division site with some degree of glycan specificity. Interestingly, YtfB also shows homology to the virulence factor OapA from Haemophilus influenzae, which is important for adherence to epithelial cells, indicating the potential of additional function(s) for YtfB. Here we show that E. coli YtfB binds to N’acetylglucosamine and mannobiose glycans with high affinity. The loss of ytfB results in a reduction in the ability of the uropathogenic E. coli strain UTI89 to adhere to human kidney cells, but not to bladder cells, suggesting a specific role in the initial adherence stage of ascending urinary tract infections. Taken together, our results suggest a role for YtfB in adhesion to specific eukaryotic cells, which may be additional, or complementary, to its role in cell division. This study highlights the importance of understanding the possible multiple functions of proteins based on homology, which may be specific to different environmental conditions.
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Affiliation(s)
- Amy L Bottomley
- ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia.
| | - Elizabeth Peterson
- ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia
| | - Gregory Iosifidis
- ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia
| | - Adeline Mei Hui Yong
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) and the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | | | - Shirin Ansari
- ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia
| | - Chris McKenzie
- ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia
| | - Catherine Burke
- ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia.,School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia
| | - Iain G Duggin
- ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia
| | - Kimberly A Kline
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) and the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Elizabeth J Harry
- ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Sydney, Australia
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16
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Kamagata K, Itoh Y, Subekti DRG. How p53 Molecules Solve the Target DNA Search Problem: A Review. Int J Mol Sci 2020; 21:E1031. [PMID: 32033163 PMCID: PMC7037437 DOI: 10.3390/ijms21031031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/11/2020] [Accepted: 01/31/2020] [Indexed: 12/14/2022] Open
Abstract
Interactions between DNA and DNA-binding proteins play an important role in many essential cellular processes. A key function of the DNA-binding protein p53 is to search for and bind to target sites incorporated in genomic DNA, which triggers transcriptional regulation. How do p53 molecules achieve "rapid" and "accurate" target search in living cells? The search dynamics of p53 were expected to include 3D diffusion in solution, 1D diffusion along DNA, and intersegmental transfer between two different DNA strands. Single-molecule fluorescence microscopy enabled the tracking of p53 molecules on DNA and the characterization of these dynamics quantitatively. Recent intensive single-molecule studies of p53 succeeded in revealing each of these search dynamics. Here, we review these studies and discuss the target search mechanisms of p53.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; (Y.I.); (D.R.G.S.)
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; (Y.I.); (D.R.G.S.)
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Dwiky Rendra Graha Subekti
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; (Y.I.); (D.R.G.S.)
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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17
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Siddiquee R, Choi SSC, Lam SS, Wang P, Qi R, Otting G, Sunde M, Kwan AHY. Cell-free expression of natively folded hydrophobins. Protein Expr Purif 2020; 170:105591. [PMID: 32032769 DOI: 10.1016/j.pep.2020.105591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 01/07/2023]
Abstract
Hydrophobins are a family of cysteine-rich proteins unique to filamentous fungi. The proteins are produced in a soluble form but self-assemble into organised amphipathic layers at hydrophilic:hydrophobic interfaces. These layers contribute to transitions between wet and dry environments, spore dispersal and attachment to surfaces for growth and infection. Hydrophobins are characterised by four disulphide bonds that are critical to their structure and function. Thus, obtaining correctly folded, soluble and functional hydrophobins directly from bacterial recombinant expression is challenging and in most cases, initial denaturation from inclusion bodies followed by oxidative refolding are required to obtain folded proteins. Here, we report the use of cell-free expression with E. coli cell lysate to directly obtain natively folded hydrophobins. All six of the hydrophobins tested could be expressed after optimisation of redox conditions. For some hydrophobins, the inclusion of the disulfide isomerase DsbC further enhanced expression levels. We are able to achieve a yield of up to 1 mg of natively folded hydrophobin per mL of reaction. This has allowed the confirmation of the correct folding of hydrophobins with the use of 15N-cysteine and 15N-1H nuclear magnetic resonance experiments within 24 h of starting from plasmid stocks.
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Affiliation(s)
- Rezwan Siddiquee
- The University of Sydney, School of Life and Environmental Sciences and SydneyNano, Australia
| | - Samuel Sung-Chan Choi
- The University of Sydney, School of Life and Environmental Sciences and SydneyNano, Australia
| | - Shirley Siuley Lam
- The University of Sydney, School of Life and Environmental Sciences and SydneyNano, Australia
| | - Patrick Wang
- The University of Sydney, School of Life and Environmental Sciences and SydneyNano, Australia
| | - Ruhu Qi
- Australian National University, Research School of Chemistry, Australia
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Australia
| | - Margaret Sunde
- The University of Sydney, School of Medical Sciences and SydneyNano, Australia
| | - Ann Hau-Yu Kwan
- The University of Sydney, School of Life and Environmental Sciences and SydneyNano, Australia.
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18
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Loan TD, Easton CJ, Alissandratos A. DNA amplification with in situ nucleoside to dNTP synthesis, using a single recombinant cell lysate of E. coli. Sci Rep 2019; 9:15621. [PMID: 31666578 PMCID: PMC6821818 DOI: 10.1038/s41598-019-51917-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/07/2019] [Indexed: 02/08/2023] Open
Abstract
Nucleic acid amplification (NAA) is a cornerstone of modern molecular and synthetic biology. Routine application by non-specialists, however, is hampered by difficulties with storing and handling the requisite labile and expensive reagents, such as deoxynucleoside triphosphates (dNTPs) and polymerases, and the complexity of protocols for their use. Here, a recombinant E. coli extract is reported that provides all the enzymes to support high-fidelity DNA amplification, and with labile dNTPs generated in situ from cheap and stable deoxynucleosides. Importantly, this is obtained from a single, engineered cell strain, through minimal processing, as a lysate capable of replacing the cold-stored commercial reagents in a typical PCR. This inexpensive preparation is highly active, as 1 L of bacterial culture is enough to supply ~106 NAA reactions. Lyophilized lysate can be used after a single-step reconstitution, resulting overall in a greatly simplified workflow and a promising synthetic biology tool, in particular for applications such as diagnostics.
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Affiliation(s)
- Thomas D Loan
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Apostolos Alissandratos
- Research School of Chemistry, Australian National University, Canberra, Australia. .,CSIRO Synthetic Biology Future Science Platform, Australian National University, Canberra, Australia.
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19
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Alfaro-Chávez AL, Liu JW, Porter JL, Goldman A, Ollis DL. Improving on nature’s shortcomings: evolving a lipase for increased lipolytic activity, expression and thermostability. Protein Eng Des Sel 2019; 32:13-24. [DOI: 10.1093/protein/gzz024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 06/30/2019] [Accepted: 07/07/2019] [Indexed: 01/18/2023] Open
Abstract
Abstract
An enzyme must be soluble, stable, active and easy to produce to be useful in industrial applications. Not all enzymes possess these attributes. We set out to determine how many changes are required to convert an enzyme with poor properties into one that has useful properties. Lipase Lip3 from Drosophila melanogaster had been previously optimised for expression in Escherichia coli. The expression levels were good, but Lip3 was mainly insoluble with poor activity. Directed evolution was used to identify variants with enhanced activity along with improved solubility. Five variants and the wild-type (wt) enzyme were purified and characterised. The yield of the wt enzyme was just 2.2 mg/L of culture, while a variant, produced under the same conditions, gave 351 mg. The improvement of activity of the best variant was 200 times higher than that of the wt when the crude lysates were analysed using pNP-C8, but with purified protein, the improvement observed was 1.5 times higher. This means that most of the increase of activity is due to increase in solubility and stability. All the purified variants showed increased thermal stability compared with the wt enzyme that had a T1/2 of 37°C, while the mutant with P291L of 42.2°C and the mutant R7_47D with five mutations had a value of 52.9°C, corresponding to an improvement of 16°C. The improved variants had between five and nine changes compared with the wt enzyme. There were four changes that were found in all 30 final round variants for which sequences were obtained; three of these changes were found in the substrate-binding domain.
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Affiliation(s)
- Ana L Alfaro-Chávez
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Jian-Wei Liu
- CSIRO Land and Water, Black Mountain, Canberra ACT 2601, Australia
| | - Joanne L Porter
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Adrian Goldman
- School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Molecular and Integrative Biosciences Program, University of Helsinki, Helsinki FIN-0018, Finland
| | - David L Ollis
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
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20
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Bahramzadeh A, Huber T, Otting G. Three-Dimensional Protein Structure Determination Using Pseudocontact Shifts of Backbone Amide Protons Generated by Double-Histidine Co 2+-Binding Motifs at Multiple Sites. Biochemistry 2019; 58:3243-3250. [PMID: 31282649 DOI: 10.1021/acs.biochem.9b00404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pseudocontact shifts (PCSs) generated by paramagnetic metal ions contribute highly informative long-range structure restraints that can be measured in solution and are ideally suited to guide structure prediction algorithms in determining global protein folds. We recently demonstrated that PCSs, which are relatively small but of high quality, can be generated by a double-histidine (dHis) motif in an α-helix, which provides a well-defined binding site for a single Co2+ ion. Here we show that PCSs of backbone amide protons generated by dHis-Co2+ motifs positioned in four different α-helices of a protein deliver excellent restraints to determine the three-dimensional (3D) structure of a protein in a way akin to the global positioning system (GPS). We demonstrate the approach with GPS-Rosetta calculations of the 3D structure of the C-terminal domain of the chaperone ERp29 (ERp29-C). Despite the relatively small size of the PCSs generated by the dHis-Co2+ motifs, the structure calculations converged readily. Generating PCSs by the dHis-Co2+ motif thus presents an excellent alternative to the use of lanthanide tags.
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Affiliation(s)
- Alireza Bahramzadeh
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Thomas Huber
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Gottfried Otting
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
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21
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Leven I, Levy Y. Quantifying the two-state facilitated diffusion model of protein-DNA interactions. Nucleic Acids Res 2019; 47:5530-5538. [PMID: 31045207 PMCID: PMC6582340 DOI: 10.1093/nar/gkz308] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/13/2019] [Accepted: 04/17/2019] [Indexed: 01/13/2023] Open
Abstract
The current report extends the facilitated diffusion model to account for conflict between the search and recognition binding modes adopted by DNA-binding proteins (DBPs) as they search DNA and subsequently recognize and bind to their specific binding site. The speed of the search dynamics is governed by the energetic ruggedness of the protein-DNA landscape, whereas the rate for the recognition process is mostly dictated by the free energy barrier for the transition between the DBP's search and recognition binding modes. We show that these two modes are negatively coupled, such that fast 1D sliding and rapid target site recognition probabilities are unlikely to coexist. Thus, a tradeoff occurs between optimizing the timescales for finding and binding the target site. We find that these two kinetic properties can be balanced to produce a fast timescale for the total target search and recognition process by optimizing frustration. Quantification of the facilitated diffusion model by including a frustration term enables it to explain several experimental observations concerning search and recognition speeds. The extended model captures experimental estimate of the energetic ruggedness of the protein-DNA landscape and predicts how various molecular properties of protein-DNA binding affect recognition kinetics. Particularly, point mutations may change the frustration and so affect protein association with DNA, thus providing a means to modulate protein-DNA affinity by manipulating the protein's association or dissociation reactions.
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Affiliation(s)
- Itai Leven
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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22
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Tsang TF, Qiu Y, Lin L, Ye J, Ma C, Yang X. Simple Method for Studying in Vitro Protein-Protein Interactions Based on Protein Complementation and Its Application in Drug Screening Targeting Bacterial Transcription. ACS Infect Dis 2019; 5:521-527. [PMID: 30834747 DOI: 10.1021/acsinfecdis.9b00020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions (PPIs) underpin essential cellular processes of all organisms and are increasingly considered as drug targets. A number of techniques have been established to study PPIs; however, development of a simple and cost-effective method for in vitro high throughput screening of PPI inhibitors is still in demand or desirable. We report herein a simple method based on protein complementation for the in vitro study of PPIs, as well as screening of inhibitors against the PPI of interest. We have validated this system utilizing bacterial transcription factors NusB and NusE. Three derivatives of an inhibitor targeting the NusB-NusE interaction were synthesized and characterized with the system, which showed specific inhibition and antimicrobial activities. We have further confirmed the system with the RNA polymerase-σ interaction and an inhibitor. This system is expected to be suitable for more extensive high throughput screening of large chemical libraries. Additionally, our vector system can be easily adapted to study other PPI pairs, followed by inhibitor screening for hit identification in the application of early stage drug discovery.
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Affiliation(s)
- Tsz Fung Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong
| | - Yangyi Qiu
- The Hong Kong Polytechnic University Shenzhen Research Institute, 18 Yue Xing 1st Road, Nanshan, Shenzhen, Guangdong 518057, China
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 11 Yuk Choi Road, Kowloon, Hong Kong
| | - Lin Lin
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong
| | - Jiqing Ye
- The Hong Kong Polytechnic University Shenzhen Research Institute, 18 Yue Xing 1st Road, Nanshan, Shenzhen, Guangdong 518057, China
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 11 Yuk Choi Road, Kowloon, Hong Kong
| | - Cong Ma
- The Hong Kong Polytechnic University Shenzhen Research Institute, 18 Yue Xing 1st Road, Nanshan, Shenzhen, Guangdong 518057, China
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 11 Yuk Choi Road, Kowloon, Hong Kong
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong
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23
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Ghodke H, Paudel BP, Lewis JS, Jergic S, Gopal K, Romero ZJ, Wood EA, Woodgate R, Cox MM, van Oijen AM. Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response. eLife 2019; 8:42761. [PMID: 30717823 PMCID: PMC6363387 DOI: 10.7554/elife.42761] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/22/2019] [Indexed: 12/14/2022] Open
Abstract
The RecA protein orchestrates the cellular response to DNA damage via its multiple roles in the bacterial SOS response. Lack of tools that provide unambiguous access to the various RecA states within the cell have prevented understanding of the spatial and temporal changes in RecA structure/function that underlie control of the damage response. Here, we develop a monomeric C-terminal fragment of the λ repressor as a novel fluorescent probe that specifically interacts with RecA filaments on single-stranded DNA (RecA*). Single-molecule imaging techniques in live cells demonstrate that RecA is largely sequestered in storage structures during normal metabolism. Upon DNA damage, the storage structures dissolve and the cytosolic pool of RecA rapidly nucleates to form early SOS-signaling complexes, maturing into DNA-bound RecA bundles at later time points. Both before and after SOS induction, RecA* largely appears at locations distal from replisomes. Upon completion of repair, RecA storage structures reform.
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Affiliation(s)
- Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Bishnu P Paudel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Kamya Gopal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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24
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Mutant T4 DNA polymerase for easy cloning and mutagenesis. PLoS One 2019; 14:e0211065. [PMID: 30673756 PMCID: PMC6343910 DOI: 10.1371/journal.pone.0211065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
The advent of high-fidelity DNA polymerases that can be used to linearize and amplify whole plasmids by PCR opened the door to greatly simplified cloning and mutagenesis protocols. Commercially available kits work well, but often have been optimized using undisclosed or proprietory components. Here we show that a mutant T4 DNA polymerase (Y320A) with attenuated 3’-exonuclease activity is uniquely suited to generate single-stranded DNA overhangs of uniform length in a more easily controllable manner than the wild-type enzyme, and this can be used to increase the yields of colonies containing correctly modified plasmids in cloning and mutagenesis experiments, which is particularly useful when E. coli cells are of relatively low competency. Standard protocols using the mutant T4 DNA polymerase are provided for the sequence and ligation independent cloning (SLIC) method and a modified QuikChange method, where the mutant enzyme enhances the yield of correctly mutated plasmid and further suppresses parental plasmid during digestion with DpnI. Single-stranded DNA overhangs generated by the mutant T4 DNA polymerase facilitate subsequent plasmid circularization, annealing and ligation in E. coli.
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25
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McGrath AE, Martyn AP, Whittell LR, Dawes FE, Beck JL, Dixon NE, Kelso MJ, Oakley AJ. Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens. J Struct Biol 2018; 204:396-405. [DOI: 10.1016/j.jsb.2018.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
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26
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Abstract
Coordination between chromosome replication and segregation is essential for equal partitioning of genetic material between daughter cells. In bacteria, this is achieved through the proximity of the origin of replication, oriC, and the chromosome partitioning site, parS We report here that in Pseudomonas aeruginosa, segregation but not replication is also controlled at the terminus region of the chromosome. Using the fluorescent repressor operator system (FROS), we investigated chromosome segregation in P. aeruginosa strain PAO1-UW, wherein the chromosome dimer resolution site, dif, is asymmetrically positioned relative to oriC In these cells, segregation proceeded sequentially along the two chromosomal arms and terminated at dif In contrast, chromosome replication terminated elsewhere, opposite from oriC We further found two large domains on the longer arm of the chromosome, wherein DNA segregated simultaneously. Notably, GC-skew, which reflects a bias in nucleotide usage between the leading and lagging strands of the chromosome, switches polarity at the dif locus but not necessarily at the terminus of replication. These data demonstrate that termination of chromosome replication and segregation can be physically separated without adverse effects on bacterial fitness. They also reveal the critical role of the dif region in defining the global layout of the chromosome and the progression of chromosome segregation and suggest that chromosome packing adapts to its subcellular layout.IMPORTANCE Segregation of genetic information is a central event in cellular life. In bacteria, chromosome segregation occurs concurrently with replication, sequentially along the two arms from oriC to dif How the two processes are coordinated is unknown. We explored here chromosome segregation in an opportunistic human pathogen, Pseudomonas aeruginosa, using its strain with markedly unequal chromosomal arms. We found that replication and segregation diverge in this strain and terminate at very different locations, whereas the longer chromosomal arm folds into large domains to align itself with the shorter arm. The significance of this research is in establishing that segregation and replication of bacterial chromosomes are largely uncoupled from each other and that the large-scale structure of the chromosome adapts to its subcellular layout.
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27
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Loan TD, Easton CJ, Alissandratos A. Recombinant cell-lysate-catalysed synthesis of uridine-5'-triphosphate from nucleobase and ribose, and without addition of ATP. N Biotechnol 2018; 49:104-111. [PMID: 30347258 DOI: 10.1016/j.nbt.2018.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 11/16/2022]
Abstract
Nucleoside triphosphates (NTPs) are important synthetic targets with diverse applications in therapeutics and diagnostics. Enzymatic routes to NTPs from simple building blocks are attractive, however the cost and complexity of assembling the requisite mixtures of multiple enzymes hinders application. Here, we describe the use of an engineered E. coli cell-free lysate as an efficient readily-prepared multi-enzyme biocatalyst for the production of uridine triphosphate (UTP) from free ribose and nucleobase. Endogenous lysate enzymes are able to support the nucleobase ribosylation and nucleotide phosphorylation steps, while uridine phosphorylation and the production of ribose phosphates (ribose 1-phosphate, ribose 5-phosphate and phosphoribosyl pyrophosphate) require recombinant enrichment of endogenous activities. Co-expression vectors encoding all required recombinant enzymes were employed for host cell transformation, such that a cell-free lysate with all necessary activities was obtained from a single bacterial culture. ATP required as phosphorylation cofactor was recycled by endogenous lysate enzymes using cheap, readily-prepared acetyl phosphate. Surprisingly, acetyl phosphate initiated spontaneous generation of ATP in the lysate, most likely from the breakdown of endogenous pools of adenosine-containing starting materials (e.g. adenosine cofactors, ribonucleic acids). The sub-stoichiometric amount of ATP produced and recycled in this way was enough to support all ATP-dependent steps without addition of any exogenous cofactor or auxiliary enzyme. Using this approach, equimolar solutions of orotic acid and ribose are transformed near quantitatively into 1.4 g L-1 UTP within 2.5 h, using a low-cost, readily-generated biocatalytic preparation.
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Affiliation(s)
- Thomas D Loan
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Apostolos Alissandratos
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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28
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Loh CT, Adams LA, Graham B, Otting G. Genetically encoded amino acids with tert-butyl and trimethylsilyl groups for site-selective studies of proteins by NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2018; 71:287-293. [PMID: 29197976 DOI: 10.1007/s10858-017-0157-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
The amino acids 4-(tert-butyl)phenylalanine (Tbf) and 4-(trimethylsilyl)phenylalanine (TMSf), as well as a partially deuterated version of Tbf (dTbf), were chemically synthesized and site-specifically incorporated into different proteins, using an amber stop codon, suppressor tRNA and the broadband aminoacyl-tRNA synthetase originally evolved for the incorporation of p-cyano-phenylalanine. The 1H-NMR signals of the tert-butyl and TMS groups were compared to the 1H-NMR signal of tert-butyltyrosine (Tby) in protein systems with molecular weights ranging from 8 to 54 kDa. The 1H-NMR resonance of the TMS group appeared near 0 ppm in a spectral region with few protein resonances, facilitating the observation of signal changes in response to ligand binding. In all proteins, the R 2 relaxation rate of the tert-butyl group of Tbf was only little greater than that of Tby (less than two-fold). Deuteration of the phenyl ring of Tbf made only a relatively small difference. The effective T 2 relaxation time of the TMS signal was longer than 140 ms even in the 54 kDa system.
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Affiliation(s)
- Choy Theng Loh
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- Zhejiang Provincial Key Laboratory of Chemical and Biological Processing Technology of Farm Products, Zhejiang University of Science and Technology, Hangzhou, 310023, People's Republic of China
| | - Luke A Adams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Bim Graham
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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29
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Welegedara AP, Adams LA, Huber T, Graham B, Otting G. Site-Specific Incorporation of Selenocysteine by Genetic Encoding as a Photocaged Unnatural Amino Acid. Bioconjug Chem 2018; 29:2257-2264. [DOI: 10.1021/acs.bioconjchem.8b00254] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Adarshi P. Welegedara
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A. Adams
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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30
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Campbell EC, Grant J, Wang Y, Sandhu M, Williams RJ, Nisbet DR, Perriman AW, Lupton DW, Jackson CJ. Hydrogel‐Immobilized Supercharged Proteins. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201700240] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Eleanor C. Campbell
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Jacob Grant
- School of Chemistry Monash University Clayton VIC 3800 Australia
| | - Yi Wang
- Laboratory of Advanced Biomaterials Research School of Engineering The Australian National University Canberra ACT 2601 Australia
| | - Mahakaran Sandhu
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | | | - David R. Nisbet
- Laboratory of Advanced Biomaterials Research School of Engineering The Australian National University Canberra ACT 2601 Australia
| | - Adam W. Perriman
- School of Cellular and Molecular Medicine University of Bristol Bristol BS8 1TD UK
| | - David W. Lupton
- School of Chemistry Monash University Clayton VIC 3800 Australia
| | - Colin J. Jackson
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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31
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Prokopiou G, Lee MD, Collauto A, Abdelkader EH, Bahrenberg T, Feintuch A, Ramirez-Cohen M, Clayton J, Swarbrick JD, Graham B, Otting G, Goldfarb D. Small Gd(III) Tags for Gd(III)–Gd(III) Distance Measurements in Proteins by EPR Spectroscopy. Inorg Chem 2018; 57:5048-5059. [DOI: 10.1021/acs.inorgchem.8b00133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgia Prokopiou
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elwy H. Abdelkader
- Research School of Chemistry, Australian National University, Canberra, ACT 2601,Australia
| | - Thorsten Bahrenberg
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marie Ramirez-Cohen
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jessica Clayton
- Department of Physics, University of California, Santa Barbara, California 93106-9530, United States
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601,Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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32
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Becker W, Adams LA, Graham B, Wagner GE, Zangger K, Otting G, Nitsche C. Trimethylsilyl tag for probing protein-ligand interactions by NMR. JOURNAL OF BIOMOLECULAR NMR 2018; 70:211-218. [PMID: 29564580 DOI: 10.1007/s10858-018-0173-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
Protein-ligand titrations can readily be monitored with a trimethylsilyl (TMS) tag. Owing to the intensity, narrow line shape and unique chemical shift of a TMS group, dissociation constants can be determined from straightforward 1D 1H-NMR spectra not only in the fast but also in the slow exchange limit. The tag is easily attached to cysteine residues and a sensitive reporter of ligand binding also at sites where it does not interfere with ligand binding or catalytic efficiency of the target protein. Its utility is demonstrated for the Zika virus NS2B-NS3 protease and the human prolyl isomerase FK506 binding protein.
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Affiliation(s)
- Walter Becker
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- Institute of Chemistry, University of Graz, 8010, Graz, Austria
| | - Luke A Adams
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010, Graz, Austria
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, 8010, Graz, Austria
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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33
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Mahawaththa MC, Lee MD, Giannoulis A, Adams LA, Feintuch A, Swarbrick JD, Graham B, Nitsche C, Goldfarb D, Otting G. Small neutral Gd(iii) tags for distance measurements in proteins by double electron–electron resonance experiments. Phys Chem Chem Phys 2018; 20:23535-23545. [DOI: 10.1039/c8cp03532f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small Gd(iii) tags based on DO3A deliver narrow and readily predictable distances by double electron–electron resonance (DEER) measurements.
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Affiliation(s)
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Angeliki Giannoulis
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Luke A. Adams
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Christoph Nitsche
- Research School of Chemistry
- The Australian National University
- Canberra
- Australia
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Gottfried Otting
- Research School of Chemistry
- The Australian National University
- Canberra
- Australia
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34
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Jabar S, Adams LA, Wang Y, Aurelio L, Graham B, Otting G. Chemical Tagging with tert-Butyl and Trimethylsilyl Groups for Measuring Intermolecular Nuclear Overhauser Effects in a Large Protein-Ligand Complex. Chemistry 2017; 23:13033-13036. [PMID: 28763128 DOI: 10.1002/chem.201703531] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 11/07/2022]
Abstract
Intermolecular 1 H-1 H nuclear Overhauser effects (NOE) present a powerful tool to assess contacts between proteins and binding partners, but are difficult to identify for complexes of high molecular weight. This report shows that intermolecular NOEs can readily be observed following chemical labeling with tert-butyl or trimethylsilyl (TMS) groups. Proteins can be furnished with tert-butyl or TMS groups site-specifically using genetically encoded unnatural amino acids or by chemical modification of single cysteine residues. No isotope labeling is required. The approach is demonstrated with the 95 kDa complex between tetrameric E. coli single-stranded DNA binding protein (SSB) and single-stranded DNA.
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Affiliation(s)
- Shereen Jabar
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A Adams
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville VIC, 3052, Australia
| | - Yao Wang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville VIC, 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville VIC, 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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35
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Welegedara AP, Yang Y, Lee MD, Swarbrick JD, Huber T, Graham B, Goldfarb D, Otting G. Double‐Arm Lanthanide Tags Deliver Narrow Gd
3+
–Gd
3+
Distance Distributions in Double Electron–Electron Resonance (DEER) Measurements. Chemistry 2017; 23:11694-11702. [DOI: 10.1002/chem.201702521] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Adarshi P. Welegedara
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Yin Yang
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Thomas Huber
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Daniella Goldfarb
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Gottfried Otting
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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36
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Mahawaththa MC, Pearce BJ, Szabo M, Graham B, Klein CD, Nitsche C, Otting G. Solution conformations of a linked construct of the Zika virus NS2B-NS3 protease. Antiviral Res 2017; 142:141-147. [DOI: 10.1016/j.antiviral.2017.03.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 03/14/2017] [Accepted: 03/18/2017] [Indexed: 01/28/2023]
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37
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Pearce BJG, Jabar S, Loh CT, Szabo M, Graham B, Otting G. Structure restraints from heteronuclear pseudocontact shifts generated by lanthanide tags at two different sites. JOURNAL OF BIOMOLECULAR NMR 2017; 68:19-32. [PMID: 28434103 DOI: 10.1007/s10858-017-0111-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/11/2017] [Indexed: 05/14/2023]
Abstract
Pseudocontact shifts (PCS) encode long-range information on 3D structures of protein backbones and side-chains. The level of structural detail that can be obtained increases with the number of different sites tagged with a paramagnetic metal ion to generate PCSs. Here we show that PCSs from two different sites can suffice to determine the structure of polypeptide chains and their location and orientation relative to the magnetic susceptibility tensor χ, provided that PCSs are available for 1H as well as heteronuclear spins. In addition, PCSs from two different sites are shown to provide detailed structural information on the conformation of methyl group-bearing amino-acid side-chains. A previously published ensemble structure of ubiquitin is shown to explain the magnetic susceptibility and alignment tensors slightly better than structures that try to explain the experimental data by a single conformation, illustrating the potential of PCSs as a tool to investigate small conformational changes.
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Affiliation(s)
- Benjamin J G Pearce
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Shereen Jabar
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Choy-Theng Loh
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Monika Szabo
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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38
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Kamagata K, Murata A, Itoh Y, Takahashi S. Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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39
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Sugrue E, Scott C, Jackson CJ. Constrained evolution of a bispecific enzyme: lessons for biocatalyst design. Org Biomol Chem 2017; 15:937-946. [DOI: 10.1039/c6ob02355j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of the natural evolution of bispecificity in triazine hydrolase highlights the importance of epistasis in protein engineering and evolution.
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Affiliation(s)
- E. Sugrue
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - C. Scott
- Commonwealth Scientific and Industrial Research Organisation
- Canberra
- Australia
| | - C. J. Jackson
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
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40
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Alissandratos A, Caron K, Loan TD, Hennessy JE, Easton CJ. ATP Recycling with Cell Lysate for Enzyme-Catalyzed Chemical Synthesis, Protein Expression and PCR. ACS Chem Biol 2016; 11:3289-3293. [PMID: 27978706 DOI: 10.1021/acschembio.6b00838] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
E. coli lysate efficiently catalyzes acetyl phosphate-driven ATP regeneration in several important biotechnological applications. The utility of this ATP recycling strategy in enzyme-catalyzed chemical synthesis is illustrated through the conversion of uridine to UMP by the lysate from recombinant overexpression of uridine kinase with the E. coli. The UMP is further transformed into UTP through sequential phosphorylations by kinases naturally present in the lysate, in high yield. Cytidine and 5-fluorouridine also give the corresponding NMPs and NTPs with this system. Cell-free protein expression with a processed extract of lysate also proceeds readily when, instead of adding the required NTPs, all four are produced in situ from the NMPs, using acetyl phosphate and relying on endogenous kinase activity. Similarly, dNMPs can be used to produce the dNTPs necessary for DNA synthesis in PCR. These cheap alternative protocols showcase the potential of acetyl phosphate and ATP recycling with readily available cell lysate.
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Affiliation(s)
| | - Karine Caron
- Research School
of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Thomas D. Loan
- Research School
of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - James E. Hennessy
- Research School
of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Christopher J. Easton
- Research School
of Chemistry, Australian National University, Canberra ACT 2601, Australia
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41
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Sugrue E, Carr PD, Scott C, Jackson CJ. Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases. Biochemistry 2016; 55:6304-6313. [DOI: 10.1021/acs.biochem.6b00731] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elena Sugrue
- Research
School of Chemistry, Australian National University, Canberra, Australia
| | - Paul D. Carr
- Research
School of Chemistry, Australian National University, Canberra, Australia
| | | | - Colin J. Jackson
- Research
School of Chemistry, Australian National University, Canberra, Australia
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42
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Moolman MC, Tiruvadi Krishnan S, Kerssemakers JWJ, de Leeuw R, Lorent V, Sherratt DJ, Dekker NH. The progression of replication forks at natural replication barriers in live bacteria. Nucleic Acids Res 2016; 44:6262-73. [PMID: 27166373 PMCID: PMC5291258 DOI: 10.1093/nar/gkw397] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 01/07/2023] Open
Abstract
Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood. By performing quantitative fluorescence microscopy with microfuidics, we investigate the effect on the replisome when encountering these barriers in live Escherichia coli cells. We make use of an E. coli variant that includes only an ectopic origin of replication that is positioned such that one of the two replisomes encounters a Tus-ter barrier before the other replisome. This enables us to single out the effect of encountering a Tus-ter roadblock on an individual replisome. We demonstrate that the replisome remains stably bound after encountering a Tus-ter complex from the non-permissive direction. Furthermore, the replisome is only transiently blocked, and continues replication beyond the barrier. Additionally, we demonstrate that these barriers affect sister chromosome segregation by visualizing specific chromosomal loci in the presence and absence of the Tus protein. These observations demonstrate the resilience of the replication fork to natural barriers and the sensitivity of chromosome alignment to fork progression.
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Affiliation(s)
- M Charl Moolman
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Sriram Tiruvadi Krishnan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Roy de Leeuw
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Vincent Lorent
- Université Paris 13, Sorbonne Paris Cité, Laboratoire de Physique des Lasers, CNRS, (UMR 7538), F-93430 Villetaneuse, France
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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43
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Fraser NJ, Liu JW, Mabbitt PD, Correy GJ, Coppin CW, Lethier M, Perugini MA, Murphy JM, Oakeshott JG, Weik M, Jackson CJ. Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability. J Mol Biol 2016; 428:2359-2371. [DOI: 10.1016/j.jmb.2016.03.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/07/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
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44
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Clifton BE, Jackson CJ. Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins. Cell Chem Biol 2016; 23:236-245. [PMID: 26853627 DOI: 10.1016/j.chembiol.2015.12.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/30/2015] [Accepted: 12/19/2015] [Indexed: 11/15/2022]
Abstract
The promiscuous functions of proteins are an important reservoir of functional novelty in protein evolution, but the molecular basis for binding promiscuity remains elusive. We used ancestral protein reconstruction to experimentally characterize evolutionary intermediates in the functional expansion of the polar amino acid-binding protein family, which has evolved to bind a variety of amino acids with high affinity and specificity. High-resolution crystal structures of an ancestral arginine-binding protein in complex with l-arginine and l-glutamine show that the promiscuous binding of l-glutamine is enabled by multi-scale conformational plasticity, water-mediated interactions, and selection of an alternative conformational substate productive for l-glutamine binding. Evolution of specialized glutamine-binding proteins from this ancestral protein was achieved by displacement of water molecules from the protein-ligand interface, reducing the entropic penalty associated with the promiscuous interaction. These results provide a structural and thermodynamic basis for the co-option of a promiscuous interaction in the evolution of binding specificity.
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Affiliation(s)
- Ben E Clifton
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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45
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O'Malley WI, Abdelkader EH, Aulsebrook ML, Rubbiani R, Loh CT, Grace MR, Spiccia L, Gasser G, Otting G, Tuck KL, Graham B. Luminescent Alkyne-Bearing Terbium(III) Complexes and Their Application to Bioorthogonal Protein Labeling. Inorg Chem 2016; 55:1674-82. [PMID: 26821062 DOI: 10.1021/acs.inorgchem.5b02605] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Two new bifunctional macrocyclic chelate ligands that form luminescent terbium(III) complexes featuring an alkyne group for conjugation to (bio)molecules via the Cu(I)-catalyzed "click" reaction were synthesized. Upon ligation, the complexes exhibit a significant luminescent enhancement when excited at the λ(max) of the "clicked" products. To demonstrate the utility of the complexes for luminescent labeling, they were conjugated in vitro to E. coli aspartate/glutamate-binding protein incorporating a genetically encoded p-azido-L-phenylalanine or p-(azidomethyl)-L-phenylalanine residue. The complexes may prove useful for time-gated assay applications.
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Affiliation(s)
- William I O'Malley
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Elwy H Abdelkader
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | | | - Riccardo Rubbiani
- Department of Chemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Choy-Theng Loh
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | - Michael R Grace
- School of Chemistry, Monash University , Clayton VIC 3800, Australia
| | - Leone Spiccia
- School of Chemistry, Monash University , Clayton VIC 3800, Australia
| | - Gilles Gasser
- Department of Chemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Gottfried Otting
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | - Kellie L Tuck
- School of Chemistry, Monash University , Clayton VIC 3800, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
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46
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Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M, Oakley AJ, Dixon NE, Hamdan SM. Replisome speed determines the efficiency of the Tus−Ter replication termination barrier. Nature 2015; 525:394-8. [DOI: 10.1038/nature14866] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/26/2015] [Indexed: 11/09/2022]
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47
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Whitfield JH, Zhang WH, Herde MK, Clifton BE, Radziejewski J, Janovjak H, Henneberger C, Jackson CJ. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Sci 2015; 24:1412-22. [PMID: 26061224 DOI: 10.1002/pro.2721] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/05/2015] [Indexed: 11/09/2022]
Abstract
Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 µM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue.
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Affiliation(s)
- Jason H Whitfield
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - William H Zhang
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Michel K Herde
- Institute of Cellular Neurosciences, University of Bonn Medical School, Bonn, Germany
| | - Ben E Clifton
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Johanna Radziejewski
- Institute of Cellular Neurosciences, University of Bonn Medical School, Bonn, Germany
| | - Harald Janovjak
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Christian Henneberger
- Institute of Cellular Neurosciences, University of Bonn Medical School, Bonn, Germany.,Institute of Neurology, University College London, London, United Kingdom
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australia
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48
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Berghuis BA, Dulin D, Xu ZQ, van Laar T, Cross B, Janissen R, Jergic S, Dixon NE, Depken M, Dekker NH. Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier. Nat Chem Biol 2015; 11:579-85. [PMID: 26147356 DOI: 10.1038/nchembio.1857] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 05/20/2015] [Indexed: 01/30/2023]
Abstract
The bidirectional replication of a circular chromosome by many bacteria necessitates proper termination to avoid the head-on collision of the opposing replisomes. In Escherichia coli, replisome progression beyond the termination site is prevented by Tus proteins bound to asymmetric Ter sites. Structural evidence indicates that strand separation on the blocking (nonpermissive) side of Tus-Ter triggers roadblock formation, but biochemical evidence also suggests roles for protein-protein interactions. Here DNA unzipping experiments demonstrate that nonpermissively oriented Tus-Ter forms a tight lock in the absence of replicative proteins, whereas permissively oriented Tus-Ter allows nearly unhindered strand separation. Quantifying the lock strength reveals the existence of several intermediate lock states that are impacted by mutations in the lock domain but not by mutations in the DNA-binding domain. Lock formation is highly specific and exceeds reported in vivo efficiencies. We postulate that protein-protein interactions may actually hinder, rather than promote, proper lock formation.
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Affiliation(s)
- Bojk A Berghuis
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Zhi-Qiang Xu
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Bronwen Cross
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
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49
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Beattie TR, Reyes-Lamothe R. A Replisome's journey through the bacterial chromosome. Front Microbiol 2015; 6:562. [PMID: 26097470 PMCID: PMC4456610 DOI: 10.3389/fmicb.2015.00562] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/21/2015] [Indexed: 01/03/2023] Open
Abstract
Genome duplication requires the coordinated activity of a multi-component machine, the replisome. In contrast to the background of metabolic diversity across the bacterial domain, the composition and architecture of the bacterial replisome seem to have suffered few changes during evolution. This immutability underlines the replisome’s efficiency in copying the genome. It also highlights the success of various strategies inherent to the replisome for responding to stress and avoiding problems during critical stages of DNA synthesis. Here we summarize current understanding of bacterial replisome architecture and highlight the known variations in different bacterial taxa. We then look at the mechanisms in place to ensure that the bacterial replisome is assembled appropriately on DNA, kept together during elongation, and disassembled upon termination. We put forward the idea that the architecture of the replisome may be more flexible that previously thought and speculate on elements of the replisome that maintain its stability to ensure a safe journey from origin to terminus.
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50
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Pandey M, Elshenawy MM, Jergic S, Takahashi M, Dixon NE, Hamdan SM, Patel SS. Two mechanisms coordinate replication termination by the Escherichia coli Tus-Ter complex. Nucleic Acids Res 2015; 43:5924-35. [PMID: 26007657 PMCID: PMC4499146 DOI: 10.1093/nar/gkv527] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/10/2015] [Indexed: 11/28/2022] Open
Abstract
The Escherichia coli replication terminator protein (Tus) binds to Ter sequences to block replication forks approaching from one direction. Here, we used single molecule and transient state kinetics to study responses of the heterologous phage T7 replisome to the Tus–Ter complex. The T7 replisome was arrested at the non-permissive end of Tus–Ter in a manner that is explained by a composite mousetrap and dynamic clamp model. An unpaired C(6) that forms a lock by binding into the cytosine binding pocket of Tus was most effective in arresting the replisome and mutation of C(6) removed the barrier. Isolated helicase was also blocked at the non-permissive end, but unexpectedly the isolated polymerase was not, unless C(6) was unpaired. Instead, the polymerase was blocked at the permissive end. This indicates that the Tus–Ter mechanism is sensitive to the translocation polarity of the DNA motor. The polymerase tracking along the template strand traps the C(6) to prevent lock formation; the helicase tracking along the other strand traps the complementary G(6) to aid lock formation. Our results are consistent with the model where strand separation by the helicase unpairs the GC(6) base pair and triggers lock formation immediately before the polymerase can sequester the C(6) base.
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Affiliation(s)
- Manjula Pandey
- Department of Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Mohamed M Elshenawy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, New South Wales 2522, Australia
| | - Masateru Takahashi
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, New South Wales 2522, Australia
| | - Samir M Hamdan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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