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Tang NC, Su JC, Shmidov Y, Kelly G, Deshpande S, Sirohi P, Peterson N, Chilkoti A. Synthetic intrinsically disordered protein fusion tags that enhance protein solubility. Nat Commun 2024; 15:3727. [PMID: 38697982 PMCID: PMC11066018 DOI: 10.1038/s41467-024-47519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
We report the de novo design of small (<20 kDa) and highly soluble synthetic intrinsically disordered proteins (SynIDPs) that confer solubility to a fusion partner with minimal effect on the activity of the fused protein. To identify highly soluble SynIDPs, we create a pooled gene-library utilizing a one-pot gene synthesis technology to create a large library of repetitive genes that encode SynIDPs. We identify three small (<20 kDa) and highly soluble SynIDPs from this gene library that lack secondary structure and have high solvation. Recombinant fusion of these SynIDPs to three known inclusion body forming proteins rescue their soluble expression and do not impede the activity of the fusion partner, thereby eliminating the need for removal of the SynIDP tag. These findings highlight the utility of SynIDPs as solubility tags, as they promote the soluble expression of proteins in E. coli and are small, unstructured proteins that minimally interfere with the biological activity of the fused protein.
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Affiliation(s)
- Nicholas C Tang
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jonathan C Su
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Yulia Shmidov
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Garrett Kelly
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Parul Sirohi
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Nikhil Peterson
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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2
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Bhan N, Callisto A, Strutz J, Glaser J, Kalhor R, Boyden ES, Church G, Kording K, Tyo KEJ. Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis. J Am Chem Soc 2021; 143:16630-16640. [PMID: 34591459 DOI: 10.1021/jacs.1c07331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Employing DNA as a high-density data storage medium has paved the way for next-generation digital storage and biosensing technologies. However, the multipart architecture of current DNA-based recording techniques renders them inherently slow and incapable of recording fluctuating signals with subhour frequencies. To address this limitation, we developed a simplified system employing a single enzyme, terminal deoxynucleotidyl transferase (TdT), to transduce environmental signals into DNA. TdT adds nucleotides to the 3'-ends of single-stranded DNA (ssDNA) in a template-independent manner, selecting bases according to inherent preferences and environmental conditions. By characterizing TdT nucleotide selectivity under different conditions, we show that TdT can encode various physiologically relevant signals such as Co2+, Ca2+, and Zn2+ concentrations and temperature changes in vitro. Further, by considering the average rate of nucleotide incorporation, we show that the resulting ssDNA functions as a molecular ticker tape. With this method we accurately encode a temporal record of fluctuations in Co2+ concentration to within 1 min over a 60 min period. Finally, we engineer TdT to allosterically turn off in the presence of a physiologically relevant concentration of calcium. We use this engineered TdT in concert with a reference TdT to develop a two-polymerase system capable of recording a single-step change in the Ca2+ signal to within 1 min over a 60 min period. This work expands the repertoire of DNA-based recording techniques by developing a novel DNA synthesis-based system that can record temporal environmental signals into DNA with a resolution of minutes.
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Affiliation(s)
- Namita Bhan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Mitolab, Cambridge, Massachusetts 02139, United States
| | - Alec Callisto
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Jonathan Strutz
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua Glaser
- Center for Theoretical Neuroscience, Columbia University, New York, New York 10027, United States
| | - Reza Kalhor
- Department of Biomedical Engineering, Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Edward S Boyden
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George Church
- Department of Biomedical Engineering, Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Konrad Kording
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
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3
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Deshpande S, Yang Y, Chilkoti A, Zauscher S. Enzymatic synthesis and modification of high molecular weight DNA using terminal deoxynucleotidyl transferase. Methods Enzymol 2019; 627:163-188. [PMID: 31630739 PMCID: PMC7241426 DOI: 10.1016/bs.mie.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The recognition that nucleic acids can be used as polymeric materials led to the blossoming of the field of DNA nanotechnology, with a broad range of applications in biotechnology, biosensors, diagnostics, and drug delivery. These applications require efficient methods to synthesize and chemically modify high molecular weight DNA. Here, we discuss terminal deoxynucleotidyl transferase (TdT)-catalyzed enzymatic polymerization (TcEP) as an alternative to conventional enzymatic and solid-phase DNA synthesis. We describe biochemical requirements for TcEP and provide step-by-step protocols to carry out TcEP in solution and from surfaces.
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Affiliation(s)
- Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Yunqi Yang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, United States; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States.
| | - Stefan Zauscher
- Department of Biomedical Engineering, Duke University, Durham, NC, United States; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States.
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4
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De novo DNA synthesis using polymerase-nucleotide conjugates. Nat Biotechnol 2018; 36:645-650. [PMID: 29912208 DOI: 10.1038/nbt.4173] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 05/22/2018] [Indexed: 01/02/2023]
Abstract
Oligonucleotides are almost exclusively synthesized using the nucleoside phosphoramidite method, even though it is limited to the direct synthesis of ∼200 mers and produces hazardous waste. Here, we describe an oligonucleotide synthesis strategy that uses the template-independent polymerase terminal deoxynucleotidyl transferase (TdT). Each TdT molecule is conjugated to a single deoxyribonucleoside triphosphate (dNTP) molecule that it can incorporate into a primer. After incorporation of the tethered dNTP, the 3' end of the primer remains covalently bound to TdT and is inaccessible to other TdT-dNTP molecules. Cleaving the linkage between TdT and the incorporated nucleotide releases the primer and allows subsequent extension. We demonstrate that TdT-dNTP conjugates can quantitatively extend a primer by a single nucleotide in 10-20 s, and that the scheme can be iterated to write a defined sequence. This approach may form the basis of an enzymatic oligonucleotide synthesizer.
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5
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Berdis AJ. DNA Polymerases That Perform Template-Independent DNA Synthesis. NUCLEIC ACID POLYMERASES 2014. [DOI: 10.1007/978-3-642-39796-7_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Boubakour-Azzouz I, Bertrand P, Claes A, Lopez BS, Rougeon F. Terminal deoxynucleotidyl transferase requires KU80 and XRCC4 to promote N-addition at non-V(D)J chromosomal breaks in non-lymphoid cells. Nucleic Acids Res 2012; 40:8381-91. [PMID: 22740656 PMCID: PMC3458542 DOI: 10.1093/nar/gks585] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Terminal deoxynucleotidyl transferase (TdT) is a DNA polymerase that increases the repertoire of antigen receptors by adding non-templated nucleotides (N-addition) to V(D)J recombination junctions. Despite extensive in vitro studies on TdT catalytic activity, the partners of TdT that enable N-addition remain to be defined. Using an intrachromosomal substrate, we show here that, in Chinese hamter ovary (CHO) cells, ectopic expression of TdT efficiently promotes N-additions at the junction of chromosomal double-strand breaks (DSBs) generated by the meganuclease I-SceI and that the size of the N-additions is comparable with that at V(D)J junctions. Importantly, no N-addition was observed in KU80- or XRCC4-deficient cells. These data show that, in a chromosomal context of non-lymphoid cells, TdT is actually able to promote N-addition at non-V(D)J DSBs, through a process that strictly requires the components of the canonical non-homologous end-joining pathway, KU80 and XRCC4.
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Romain F, Barbosa I, Gouge J, Rougeon F, Delarue M. Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region. Nucleic Acids Res 2009; 37:4642-56. [PMID: 19502493 PMCID: PMC2724280 DOI: 10.1093/nar/gkp460] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 12/31/2022] Open
Abstract
Terminal deoxynucleotidyltransferase (Tdt) and DNA polymerase mu (pol mu) are two eukaryotic highly similar proteins involved in DNA processing and repair. Despite their high sequence identity, they differ widely in their activity: pol mu has a templated polymerase activity, whereas Tdt has a non-templated one. Loop1, first described when the Tdt structure was solved, has been invoked as the major structural determinant of this difference. Here we describe attempts to transform Tdt into pol mu with the minimal number of mutations in and around Loop1. First we describe the effect of mutations on six different positions chosen to destabilize Tdt Loop1 structure, either by alanine substitution or by deletion; they result at most in a reduction of Tdt activity, but adding Co(++) restores most of this Tdt activity. However, a deletion of the entire Loop1 as in pol lambda does confer a limited template-dependent polymerase behavior to Tdt while a chimera bearing an extended pol mu Loop1 reproduces pol mu behavior. Finally, 16 additional substitutions are reported, targeted at the two so-called 'sequence determinant' regions located just after Loop1 or underneath. Among them, the single-point mutant F401A displays a sequence-specific replicative polymerase phenotype that is stable upon Co(++) addition. These results are discussed in light of the available crystal structures.
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Affiliation(s)
- Félix Romain
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Isabelle Barbosa
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Jérôme Gouge
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - François Rougeon
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules and URA 2581 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
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Motea EA, Berdis AJ. Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1151-66. [PMID: 19596089 DOI: 10.1016/j.bbapap.2009.06.030] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/27/2009] [Accepted: 06/30/2009] [Indexed: 01/06/2023]
Abstract
Nearly every DNA polymerase characterized to date exclusively catalyzes the incorporation of mononucleotides into a growing primer using a DNA or RNA template as a guide to direct each incorporation event. There is, however, one unique DNA polymerase designated terminal deoxynucleotidyl transferase that performs DNA synthesis using only single-stranded DNA as the nucleic acid substrate. In this chapter, we review the biological role of this enigmatic DNA polymerase and the biochemical mechanism for its ability to perform DNA synthesis in the absence of a templating strand. We compare and contrast the molecular events for template-independent DNA synthesis catalyzed by terminal deoxynucleotidyl transferase with other well-characterized DNA polymerases that perform template-dependent synthesis. This includes a quantitative inspection of how terminal deoxynucleotidyl transferase binds DNA and dNTP substrates, the possible involvement of a conformational change that precedes phosphoryl transfer, and kinetic steps that are associated with the release of products. These enzymatic steps are discussed within the context of the available structures of terminal deoxynucleotidyl transferase in the presence of DNA or nucleotide substrate. In addition, we discuss the ability of proteins involved in replication and recombination to regulate the activity of the terminal deoxynucleotidyl transferase. Finally, the biomedical role of this specialized DNA polymerase is discussed focusing on its involvement in cancer development and its use in biomedical applications such as labeling DNA for detecting apoptosis.
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Affiliation(s)
- Edward A Motea
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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9
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Fowler JD, Suo Z. Biochemical, structural, and physiological characterization of terminal deoxynucleotidyl transferase. Chem Rev 2007; 106:2092-110. [PMID: 16771444 DOI: 10.1021/cr040445w] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jason D Fowler
- Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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10
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Aminian M, Sivam S, Lee CW, Halperin SA, Lee SF. Expression and purification of a trivalent pertussis toxin-diphtheria toxin-tetanus toxin fusion protein in Escherichia coli. Protein Expr Purif 2006; 51:170-8. [PMID: 16950635 DOI: 10.1016/j.pep.2006.07.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 07/17/2006] [Accepted: 07/24/2006] [Indexed: 10/24/2022]
Abstract
Pertussis toxoid, diphtheria toxoid, and tetanus toxoid are key components of diphtheria-tetanus-acellular pertussis vaccines. The efficacy of the vaccines is well documented, however, the vaccines are expensive partly because the antigens are derived from three different bacteria. In this study, a fusion protein (PDT) composed of the immunoprotective S1 fragment of pertussis toxin, the full-length non-toxic diphtheria toxin, and fragment C of tetanus toxin was constructed via genetic means. The correct fusion was verified by restriction endonuclease analysis and Western immunoblotting. Escherichia coli carrying the recombinant plasmid (pCoPDT) produced a 161kDa protein that was recognized by antibodies specific to the three toxins. The expression of the PDT protein was inducible by isopropyl-beta-d-thio-galactoside but the total amount of protein produced was relatively low. Attempts to improve the protein yield by expression in an E. coli strain (Rosetta-gami 2) that could alleviate rare-codon usage bias and by supplementation of the growth media with amino acids deemed to be a limiting factor in translation were not successful. The PDT protein remained in the insoluble fraction when the recombinant E. coli was grown at 37 degrees C but the protein became soluble when the bacteria were grown at 22 degrees C. The PDT protein was isolated via affinity chromatography on a NiCAM column. The protein was associated with five other proteins via disulfide bonds and non-covalent interactions. Following treatment with beta-mercaptoethanol, the PDT fusion was purified to homogeneity by preparative polyacrylamide gel electrophoresis with a yield of 45 microg/L of culture. Antisera generated against the purified PDT protein recognized the native toxins indicating that some, if not all, of the native epitopes were conserved.
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Affiliation(s)
- Mahdi Aminian
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada B3H 3J5
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11
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Abstract
A number of research laboratories have investigated the properties of multichromophore molecules and their applications in materials science and in biotechnology. Previous approaches for preparing such molecules have involved traditional organic synthesis. Here we describe the one-step enzymatic synthesis of such a multichromophore species by using a DNA-polymerizing enzyme (terminal deoxynucleotidyl transferase (TdT)). We find that a nucleotide-like molecule with pyrene replacing the DNA base (dPTP) can be accepted as a substrate for this enzyme to produce discrete chromophores that have 3 or 4 pyrenes consecutively, depending on which anomer (alpha or beta) is used. Products were characterized by gel electrophoresis, mass spectrometry, and fluorescence. The reaction was found to change the fluorescence emission of the chromophore from a maximum at 375 nm (the monomer nucleotide) to 490 nm in the oligomeric product. This new green-white emission is consistent with the formation of a pyrene excimer between adjacent pyrene glycosides, which exhibit a large Stokes shift of 130 nm. The enzymatic synthesis of the pyrene excimer might have applications in homogeneous biological assays for DNA fragments, such as those that arise during apoptosis.
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Affiliation(s)
- Younjin Cho
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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12
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Doyen N, Boulé JB, Rougeon F, Papanicolaou C. Evidence that the long murine terminal deoxynucleotidyltransferase isoform plays no role in the control of V(D)J junctional diversity. THE JOURNAL OF IMMUNOLOGY 2004; 172:6764-7. [PMID: 15153493 DOI: 10.4049/jimmunol.172.11.6764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Two TdT isoforms have been found in the mouse. The short isoform is known to add N regions to gene segment junctions during V(D)J recombination, but the role of the long (TdTL) isoform is controversial. We have shown that TdTL, although endowed with terminal transferase activity, is thermally unstable and unable to add N regions in vivo. In this study, we demonstrate that TdTL is devoid of 3'-5' exonuclease activity, and provide an analysis of nucleotide deletion and addition patterns in large series of V(D)J coding joins, arguing against a role of TdTL in the control of junctional diversity in Igs and TCRs.
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Affiliation(s)
- Noëlle Doyen
- Unité de Génétique et Biochimie du Développement, Unité de Recherche Associée Centre National de la Recherche Scientifique 2581, Institut Pasteur, Paris, France
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13
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Nakashima N, Tamura T. A novel system for expressing recombinant proteins over a wide temperature range from 4 to 35°C. Biotechnol Bioeng 2004; 86:136-48. [PMID: 15052633 DOI: 10.1002/bit.20024] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Escherichia coli cells are the most commonly used host cells for large-scale production of recombinant proteins, but some proteins are difficult to express in E. coli. Therefore, we tested the nocardioform actinomycete Rhodococcus erythropolis, which grows at temperatures ranging from 4 to 35 degrees C, as an expression host cell. We constructed inducible expression vectors, where the expression of the target genes could be controlled with the antibiotic thiostrepton. Using these expression vectors, several milligrams of reporter proteins could be isolated from 1 liter of culture of R. erythropolis cells grown at a temperature range from 4 to 35 degrees C. Moreover, we successfully purified serum amyloid A1, NADH dehydorogenase 1 alpha subcomplex 4, cytochrome b5-like protein, apolipoprotein A-V, cathepsin D, pancreatic Rnase, and HMG-1 that are all difficult to express in E. coli. In the case of kallikrein 6, mouse deoxyribonuclease I and Kid1, which are also difficult to express in E. coli, the expression level of each protein increased when proteins were expressed at low temperature (4 degrees C). Based on these results, we conclude that a recombinant protein expression system using R. erythropolis as the host cell is superior to respective E. coli systems.
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Affiliation(s)
- Nobutaka Nakashima
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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14
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Delarue M, Boulé J, Lescar J, Expert-Bezançon N, Jourdan N, Sukumar N, Rougeon F, Papanicolaou C. Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase. EMBO J 2002; 21:427-39. [PMID: 11823435 PMCID: PMC125842 DOI: 10.1093/emboj/21.3.427] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The crystal structure of the catalytic core of murine terminal deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical DNA polymerase beta-like fold locked in a closed form. In addition, the structures of two different binary complexes, one with an oligonucleotide primer and the other with an incoming ddATP-Co(2+) complex, show that the substrates and the two divalent ions in the catalytic site are positioned in TdT in a manner similar to that described for the human DNA polymerase beta ternary complex, suggesting a common two metal ions mechanism of nucleotidyl transfer in these two proteins. The inability of TdT to accommodate a template strand can be explained by steric hindrance at the catalytic site caused by a long lariat-like loop, which is absent in DNA polymerase beta. However, displacement of this discriminating loop would be sufficient to unmask a number of evolutionarily conserved residues, which could then interact with a template DNA strand. The present structure can be used to model the recently discovered human polymerase mu, with which it shares 43% sequence identity.
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Affiliation(s)
- M. Delarue
- Unité de Biochimie Structurale, URA 2185 du CNRS,
Unité de Biochimie et de Génétique du Développement, URA 1960 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris and CERMAV, UPR 5301 du CNRS, 601 rue de la Chimie, 38041 Grenoble cedex 9 and Joint Structural Biology Group, ESRF, Grenoble, France Corresponding author e-mail:
| | - J.B. Boulé
- Unité de Biochimie Structurale, URA 2185 du CNRS,
Unité de Biochimie et de Génétique du Développement, URA 1960 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris and CERMAV, UPR 5301 du CNRS, 601 rue de la Chimie, 38041 Grenoble cedex 9 and Joint Structural Biology Group, ESRF, Grenoble, France Corresponding author e-mail:
| | - J. Lescar
- Unité de Biochimie Structurale, URA 2185 du CNRS,
Unité de Biochimie et de Génétique du Développement, URA 1960 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris and CERMAV, UPR 5301 du CNRS, 601 rue de la Chimie, 38041 Grenoble cedex 9 and Joint Structural Biology Group, ESRF, Grenoble, France Corresponding author e-mail:
| | | | | | | | - F. Rougeon
- Unité de Biochimie Structurale, URA 2185 du CNRS,
Unité de Biochimie et de Génétique du Développement, URA 1960 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris and CERMAV, UPR 5301 du CNRS, 601 rue de la Chimie, 38041 Grenoble cedex 9 and Joint Structural Biology Group, ESRF, Grenoble, France Corresponding author e-mail:
| | - C. Papanicolaou
- Unité de Biochimie Structurale, URA 2185 du CNRS,
Unité de Biochimie et de Génétique du Développement, URA 1960 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris and CERMAV, UPR 5301 du CNRS, 601 rue de la Chimie, 38041 Grenoble cedex 9 and Joint Structural Biology Group, ESRF, Grenoble, France Corresponding author e-mail:
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15
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Boulé JB, Rougeon F, Papanicolaou C. Terminal deoxynucleotidyl transferase indiscriminately incorporates ribonucleotides and deoxyribonucleotides. J Biol Chem 2001; 276:31388-93. [PMID: 11406636 DOI: 10.1074/jbc.m105272200] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Terminal deoxynucleotidyl transferase (TdT) catalyzes the condensation of deoxyribonucleotides on 3'-hydroxyl ends of DNA strands in a template-independent manner and adds N-regions to gene segment junctions during V(D)J recombination. Although TdT is able to incorporate a few ribonucleotides in vitro, TdT discrimination between ribo- and deoxyribonucleotides has never been studied. We found that TdT shows only a minor preference for incorporation of deoxyribonucleotides over ribonucleotides on DNA strands. However, incorporation of ribonucleotides alone or in the presence of deoxyribonucleotides generally leads to premature chain termination, reflecting an impeded accommodation of ribo- or mixed ribo/deoxyribonucleic acid substrates by TdT. An essential catalytic aspartate in TdT was identified, which is a first step toward understanding the apparent lack of sugar discrimination by TdT.
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Affiliation(s)
- J B Boulé
- Unité de Génétique et Biochimie du Développement, URA CNRS 1960, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
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16
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Boulé JB, Rougeon F, Papanicolaou C. Comparison of the two murine terminal [corrected] deoxynucleotidyltransferase terminal isoforms. A 20-amino acid insertion in the highly conserved carboxyl-terminal region modifies the thermosensitivity but not the catalytic activity. J Biol Chem 2000; 275:28984-8. [PMID: 10878023 DOI: 10.1074/jbc.m005544200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Terminal deoxynucleotidyltransferase (TdT) catalyzes the addition of nucleotides to 3'-hydroxyl ends of DNA strands in a template-independent manner and has been shown to add N-regions to gene segment junctions during V(D)J recombination. TdT is highly conserved in all vertebrate species, with a second isoform, characterized by a 20-amino acid insertion near the COOH-terminal end, described only in the mouse. The two murine isoforms differ in their subcellular localization, and the long isoform (TdTL) has previously been found to be unable to add N-regions. Using purified protein produced in a high level expression system in Escherichia coli, we were able to carry out detailed catalytic comparisons of these two TdT isoforms. We discovered that TdTL exhibits terminal transferase activity with kinetic parameters similar to those of the conserved TdT isoform (TdTS). We observed, however, that TdTL is inactivated at physiologic temperature but stable at lower temperatures. This thermal sensitivity of TdTL polymerase activity is not correlated with a significant change in the circular dichroism spectrum of the protein. Thus, the 20-amino acid insertion in TdTL does not affect the catalytic activity but modifies the thermosensitivity.
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Affiliation(s)
- J B Boulé
- Unité de Génétique et Biochimie du Développement, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
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