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Koutsogiannis Z, Mina JG, Albus CA, Kol MA, Holthuis JM, Pohl E, Denny PW. Toxoplasma ceramide synthases: Gene duplication, functional divergence, and roles in parasite fitness. FASEB J 2023; 37:e23229. [PMID: 37795915 PMCID: PMC10946778 DOI: 10.1096/fj.202201603rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 08/16/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Toxoplasma gondii is an obligate, intracellular apicomplexan protozoan parasite of both humans and animals that can cause fetal damage and abortion and severe disease in the immunosuppressed. Sphingolipids have indispensable functions as signaling molecules and are essential and ubiquitous components of eukaryotic membranes that are both synthesized and scavenged by the Apicomplexa. Ceramide is the precursor for all sphingolipids, and here we report the identification, localization and analyses of the Toxoplasma ceramide synthases TgCerS1 and TgCerS2. Interestingly, we observed that while TgCerS1 was a fully functional orthologue of the yeast ceramide synthase (Lag1p) capable of catalyzing the conversion of sphinganine to ceramide, in contrast TgCerS2 was catalytically inactive. Furthermore, genomic deletion of TgCerS1 using CRISPR/Cas-9 led to viable but slow-growing parasites indicating its importance but not indispensability. In contrast, genomic knock out of TgCerS2 was only accessible utilizing the rapamycin-inducible Cre recombinase system. Surprisingly, the results demonstrated that this "pseudo" ceramide synthase, TgCerS2, has a considerably greater role in parasite fitness than its catalytically active orthologue (TgCerS1). Phylogenetic analyses indicated that, as in humans and plants, the ceramide synthase isoforms found in Toxoplasma and other Apicomplexa may have arisen through gene duplication. However, in the Apicomplexa the duplicated copy is hypothesized to have subsequently evolved into a non-functional "pseudo" ceramide synthase. This arrangement is unique to the Apicomplexa and further illustrates the unusual biology that characterize these protozoan parasites.
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Affiliation(s)
| | - John G. Mina
- Department of BiosciencesDurham UniversityDurhamUK
| | | | - Matthijs A. Kol
- Molecular Cell Biology Division, Department of Biology/ChemistryUniversity of OsnabrückOsnabrückGermany
| | - Joost C. M. Holthuis
- Molecular Cell Biology Division, Department of Biology/ChemistryUniversity of OsnabrückOsnabrückGermany
| | - Ehmke Pohl
- Department of BiosciencesDurham UniversityDurhamUK
- Department of ChemistryDurham UniversityDurhamUK
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Takasuka TE, Kim H, Deng K, Bianchetti CM, Yamashita K, Beebe ET, Bergeman LF, Vander Meulen KA, Deutsch S, Ralph J, Adams PD, Northen TR, Fox BG. Quantitative Analysis of The High-Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase. Chembiochem 2023; 24:e202300357. [PMID: 37402642 DOI: 10.1002/cbic.202300357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
Kelp is an abundant, farmable biomass-containing laminarin and alginate as major polysaccharides, providing an excellent model substrate to study their deconstruction by simple enzyme mixtures. Our previous study showed strong reactivity of the glycoside hydrolase family 55 during hydrolysis of purified laminarin, raising the question of its reactivity with intact kelp. In this study, we determined that a combination of a single glycoside hydrolase family 55 β-1,3-exoglucanase with a broad-specificity alginate lyase from the polysaccharide lyase family 18 gives efficient hydrolysis of untreated kelp to a mixture of simple sugars, that is, glucose, gentiobiose, mannitol-end glucose, and mannuronic and guluronic acids and their soluble oligomers. Quantitative assignments from nanostructure initiator mass spectrometry (NIMS) and 2D HSQC NMR spectroscopy and analysis of the reaction time-course are provided. The data suggest that binary combinations of enzymes targeted to the unique polysaccharide composition of marine biomass are sufficient to deconstruct kelp into soluble sugars for microbial fermentation.
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Affiliation(s)
- Taichi E Takasuka
- Research Faculty of Agriculture and, Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
- Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hoon Kim
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Present address: U.S. Department of Agriculture, Forest Service, Forest Products Laboratory, 1 Gifford Pinchot Drive, Madison, WI 53726, USA
| | - Kai Deng
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA 94551, USA
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
| | - Christopher M Bianchetti
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kaho Yamashita
- Research Faculty of Agriculture and, Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
| | - Emily T Beebe
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Lai F Bergeman
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Kirk A Vander Meulen
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Samuel Deutsch
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA 94551, USA
| | - John Ralph
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brian G Fox
- Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Chae YK, Um Y, Kim H. A simple and sensitive detection of the binding ligands by using the receptor aggregation and NMR spectroscopy: a test case of the maltose binding protein. JOURNAL OF BIOMOLECULAR NMR 2021; 75:371-381. [PMID: 34524563 PMCID: PMC8441238 DOI: 10.1007/s10858-021-00381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Protein-ligand interaction is one of the highlights of molecular recognition. The most popular application of this type of interaction is drug development which requires a high throughput screening of a ligand that binds to the target protein. Our goal was to find a binding ligand with a simple detection, and once this type of ligand was found, other methods could then be used to measure the detailed kinetic or thermodynamic parameters. We started with the idea that the ligand NMR signal would disappear if it was bound to the non-tumbling mass. In order to create the non-tumbling mass, we tried the aggregates of a target protein, which was fused to the elastin-like polypeptide. We chose the maltose binding proteinas a test case, and we tried it with several sugars, which included maltose, glucose, sucrose, lactose, galactose, maltotriose, and β-cyclodextrin. The maltose signal in the H-1 NMR spectrum disappeared completely as hoped around the protein to ligand ratio of 1:3 at 298 K where the proteins aggregated. The protein signals also disappeared upon aggregation except for the fast-moving part, which resulted in a cleaner background than the monomeric form. Since we only needed to look for a disappearing signal amongst those from the mixture, it should be useful in high throughput screening. Other types of sugars except for the maltotriose and β-cyclodextrin, which are siblings of the maltose, did not seem to bind at all. We believe that our system would be especially more effective when dealing with a smaller target protein, so both the protein and the bound ligand would lose their signals only when the aggregates formed. We hope that our proposed method would contribute to accelerating the development of the potent drug candidates by simultaneously identifying several binders directly from a mixture.
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Affiliation(s)
- Young Kee Chae
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul, 05006, Korea.
| | - Yoonjin Um
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul, 05006, Korea
| | - Hakbeom Kim
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul, 05006, Korea
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Chae YK, Kim H. Development of an Autoinducible Plasmid for Recombinant Protein Production. Protein Pept Lett 2021; 28:1398-1407. [PMID: 34749604 DOI: 10.2174/0929866528666211105113750] [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: 06/14/2021] [Revised: 08/09/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The production of recombinant proteins in E. coli involves such factors as host strains, expression vectors, culture media, and induction methods. The typical procedure to produce heterologous proteins consists of the following: (1) insertion of the target gene into a suitable vector to construct an overexpression plasmid, (2) transformation of a strain specialized for protein production with the constructed plasmid DNA, (3) growth of the host in a suitable medium and induction of the protein production at a right moment, and (4) further growth to get the maximum yield. There are hurdles involved in each of these steps, and researchers have developed many materials or methods, which often require special recipes or procedures. OBJECTIVE To eliminate the special requirements for the recombinant protein production by using readily available materials. Also to save time and effort in the routine protein production work. METHOD We started with a vector capable of producing a target protein fused to the C-terminus of the maltose binding protein (MBP). The mCherry (red fluorescent protein) gene was fused to MBP. It acted as a reporter in the initial screening procedure. The original lethal gene (barnase) was replaced with sacB. We chose 3 stationary phase promoters, and made hybrids of them by mixing halves from each one. The T5 promoter was replaced with these stationary phase promoters or their hybrids. The best plasmid was selected by the color intensity of the cell pellet. MBP and GST genes were inserted in place of sacB, and their production yields were compared with the original plasmid in the conventional way of expression. RESULTS We constructed an expression plasmid with an autoinducible promoter working in a host that was not specially designed for protein production and in a TB medium which did not contain any secret ingredient, nor was difficult to prepare unlike Studier's defined medium. This plasmid also contains a color indicator which turns red when protein production is successful. We tested our system with the maltose binding protein (MBP) and the glutathione S-transferase (GST), and showed that both proteins were produced to a level comparable to what the commercial medium and/or the specialized strain yielded. CONCLUSION We developed a plasmid equipped with an autoinducible promoter, a hybrid of the two promoters which were activated at the stationary phase. This plasmid does not need a special E. coli strain nor a sophisticated nor an expensive medium. It produces an intense red (or pink) color, which can be used as an indicator of a successful production of the target protein and as a predictive measure of the amount of the produced target protein. We speculate that this plasmid will have its greatest advantage when growing cells at low temperatures which would inevitably take a long time. .
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Affiliation(s)
- Young Kee Chae
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul. Korea
| | - Hakbeom Kim
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul. Korea
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Chae YK, Kim SH, Um Y. Relationship between Protein Expression Pattern and Host Metabolome Perturbation as Monitored by Two‐Dimensional NMR Spectroscopy. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Young Kee Chae
- Department of ChemistrySejong University Seoul 05006 Korea
| | - Seol Hyun Kim
- Department of ChemistrySejong University Seoul 05006 Korea
| | - Yoonjin Um
- Department of ChemistrySejong University Seoul 05006 Korea
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6
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Frederick RO, Haruta M, Tonelli M, Lee W, Cornilescu G, Cornilescu CC, Sussman MR, Markley JL. Function and solution structure of the Arabidopsis thaliana RALF8 peptide. Protein Sci 2019; 28:1115-1126. [PMID: 31004454 PMCID: PMC6511734 DOI: 10.1002/pro.3628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/31/2022]
Abstract
We report the recombinant preparation from Escherichia coli cells of samples of two closely related, small, secreted cysteine-rich plant peptides: rapid alkalinization factor 1 (RALF1) and rapid alkalinization factor 8 (RALF8). Purified samples of the native sequence of RALF8 exhibited well-resolved nuclear magnetic resonance (NMR) spectra and also biological activity through interaction with a plant receptor kinase, cytoplasmic calcium mobilization, and in vivo root growth suppression. By contrast, RALF1 could only be isolated from inclusion bodies as a construct containing an N-terminal His-tag; its poorly resolved NMR spectrum was indicative of aggregation. We prepared samples of the RALF8 peptide labeled with 15 N and 13 C for NMR analysis and obtained near complete 1 H, 13 C, and 15 N NMR assignments; determined the disulfide pairing of its four cysteine residues; and examined its solution structure. RALF8 is mostly disordered except for the two loops spanned by each of its two disulfide bridges.
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Affiliation(s)
- Ronnie O. Frederick
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Miyoshi Haruta
- Biotechnology CenterUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Marco Tonelli
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Woonghee Lee
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Claudia C. Cornilescu
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Michael R. Sussman
- Biotechnology CenterUniversity of Wisconsin‐MadisonMadisonWisconsin53706
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - John L. Markley
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWisconsin53706
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7
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Veling MT, Reidenbach AG, Freiberger EC, Kwiecien NW, Hutchins PD, Drahnak MJ, Jochem A, Ulbrich A, Rush MJP, Russell JD, Coon JJ, Pagliarini DJ. Multi-omic Mitoprotease Profiling Defines a Role for Oct1p in Coenzyme Q Production. Mol Cell 2017; 68:970-977.e11. [PMID: 29220658 DOI: 10.1016/j.molcel.2017.11.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/29/2017] [Accepted: 11/16/2017] [Indexed: 01/08/2023]
Abstract
Mitoproteases are becoming recognized as key regulators of diverse mitochondrial functions, although their direct substrates are often difficult to discern. Through multi-omic profiling of diverse Saccharomyces cerevisiae mitoprotease deletion strains, we predicted numerous associations between mitoproteases and distinct mitochondrial processes. These include a strong association between the mitochondrial matrix octapeptidase Oct1p and coenzyme Q (CoQ) biosynthesis-a pathway essential for mitochondrial respiration. Through Edman sequencing and in vitro and in vivo biochemistry, we demonstrated that Oct1p directly processes the N terminus of the CoQ-related methyltransferase, Coq5p, which markedly improves its stability. A single mutation to the Oct1p recognition motif in Coq5p disrupted its processing in vivo, leading to CoQ deficiency and respiratory incompetence. This work defines the Oct1p processing of Coq5p as an essential post-translational event for proper CoQ production. Additionally, our data visualization tool enables efficient exploration of mitoprotease profiles that can serve as the basis for future mechanistic investigations.
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Affiliation(s)
- Mike T Veling
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew G Reidenbach
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Elyse C Freiberger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Arne Ulbrich
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew J P Rush
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jason D Russell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI 53715, USA; Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, Wilkerson EM, Johnson IE, Bingman CA, Markley JL, Coon JJ, Dal Peraro M, Pagliarini DJ. Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family. Cell Chem Biol 2017; 25:154-165.e11. [PMID: 29198567 DOI: 10.1016/j.chembiol.2017.11.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/10/2017] [Accepted: 11/01/2017] [Indexed: 12/14/2022]
Abstract
Human COQ8A (ADCK3) and Saccharomyces cerevisiae Coq8p (collectively COQ8) are UbiB family proteins essential for mitochondrial coenzyme Q (CoQ) biosynthesis. However, the biochemical activity of COQ8 and its direct role in CoQ production remain unclear, in part due to lack of known endogenous regulators of COQ8 function and of effective small molecules for probing its activity in vivo. Here, we demonstrate that COQ8 possesses evolutionarily conserved ATPase activity that is activated by binding to membranes containing cardiolipin and by phenolic compounds that resemble CoQ pathway intermediates. We further create an analog-sensitive version of Coq8p and reveal that acute chemical inhibition of its endogenous activity in yeast is sufficient to cause respiratory deficiency concomitant with CoQ depletion. Collectively, this work defines lipid and small-molecule modulators of an ancient family of atypical kinase-like proteins and establishes a chemical genetic system for further exploring the mechanistic role of COQ8 in CoQ biosynthesis.
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Affiliation(s)
- Andrew G Reidenbach
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zachary A Kemmerer
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Deniz Aydin
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Molly T McDevitt
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jaime L Stark
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jonathan A Stefely
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Thiru Reddy
- Morgridge Institute for Research, Madison, WI 53715, USA
| | | | - Emily M Wilkerson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Isabel E Johnson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Chae YK, Kim SH, Markley JL. Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy. PLoS One 2017; 12:e0177233. [PMID: 28486539 PMCID: PMC5423636 DOI: 10.1371/journal.pone.0177233] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/24/2017] [Indexed: 12/03/2022] Open
Abstract
Escherichia coli has been the most widely used host to produce large amounts of heterologous proteins. However, given an input plasmid DNA, E. coli may produce soluble protein, produce only inclusion bodies, or yield little or no protein at all. Many efforts have been made to surmount these problems, but most of them have involved time-consuming and labor-intensive trial-and-error. We hypothesized that different metabolomic fingerprints might be associated with different protein production outcomes. If so, then it might be possible to change the expression pattern by manipulating the metabolite environment. As a first step in testing this hypothesis, we probed a subset of the intracellular metabolites by partially labeling it with 13C-glucose. We tested 71 genes and identified 17 metabolites by employing the two-dimensional NMR spectroscopy. The statistical analysis showed that there existed the metabolite compositions favoring protein production. We hope that this work would help devise a systematic and predictive approach to the recombinant protein production.
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Affiliation(s)
- Young Kee Chae
- Department of Chemistry, Sejong University, Seoul, Korea
- * E-mail:
| | - Seol Hyun Kim
- Department of Chemistry, Sejong University, Seoul, Korea
| | - John L. Markley
- Department of Biochemistry, University of Wisconsin – Madison, Wisconsin, United States of America
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Walker JA, Pattathil S, Bergeman LF, Beebe ET, Deng K, Mirzai M, Northen TR, Hahn MG, Fox BG. Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:31. [PMID: 28184246 PMCID: PMC5288845 DOI: 10.1186/s13068-017-0703-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/06/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Glycoside hydrolases (GHs) are enzymes that hydrolyze polysaccharides into simple sugars. To better understand the specificity of enzyme hydrolysis within the complex matrix of polysaccharides found in the plant cell wall, we studied the reactions of individual enzymes using glycome profiling, where a comprehensive collection of cell wall glycan-directed monoclonal antibodies are used to detect polysaccharide epitopes remaining in the walls after enzyme treatment and quantitative nanostructure initiator mass spectrometry (oxime-NIMS) to determine soluble sugar products of their reactions. RESULTS Single, purified enzymes from the GH5_4, GH10, and GH11 families of glycoside hydrolases hydrolyzed hemicelluloses as evidenced by the loss of specific epitopes from the glycome profiles in enzyme-treated plant biomass. The glycome profiling data were further substantiated by oxime-NIMS, which identified hexose products from hydrolysis of cellulose, and pentose-only and mixed hexose-pentose products from the hydrolysis of hemicelluloses. The GH10 enzyme proved to be reactive with the broadest diversity of xylose-backbone polysaccharide epitopes, but was incapable of reacting with glucose-backbone polysaccharides. In contrast, the GH5 and GH11 enzymes studied here showed the ability to react with both glucose- and xylose-backbone polysaccharides. CONCLUSIONS The identification of enzyme specificity for a wide diversity of polysaccharide structures provided by glycome profiling, and the correlated identification of soluble oligosaccharide hydrolysis products provided by oxime-NIMS, offers a unique combination to understand the hydrolytic capabilities and constraints of individual enzymes as they interact with plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Sivakumar Pattathil
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Lai F. Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Emily T. Beebe
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Kai Deng
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
| | - Maryam Mirzai
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Trent R. Northen
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Michael G. Hahn
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Brian G. Fox
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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11
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Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol 2015; 3:165. [PMID: 26579511 PMCID: PMC4621489 DOI: 10.3389/fbioe.2015.00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022] Open
Abstract
Chemically synthesized nanostructure-initiator mass spectrometry (NIMS) probes derivatized with tetrasaccharides were used to study the reactivity of representative Clostridium thermocellum β-glucosidase, endoglucanases, and cellobiohydrolase. Diagnostic patterns for reactions of these different classes of enzymes were observed. Results show sequential removal of glucose by the β-glucosidase and a progressive increase in specificity of reaction from endoglucanases to cellobiohydrolase. Time-dependent reactions of these polysaccharide-selective enzymes were modeled by numerical integration, which provides a quantitative basis to make functional distinctions among a continuum of naturally evolved catalytic properties. Consequently, our method, which combines automated protein translation with high-sensitivity and time-dependent detection of multiple products, provides a new approach to annotate glycoside hydrolase phylogenetic trees with functional measurements.
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Affiliation(s)
- Kai Deng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Taichi E Takasuka
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Christopher M Bianchetti
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Chemistry, University of Wisconsin-Oshkosh , Oshkosh, WI , USA
| | - Lai F Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Brian G Fox
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Biochemistry, University of Wisconsin-Madison , Madison, WI , USA
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12
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Acheson JF, Moseson H, Fox BG. Structure of T4moF, the Toluene 4-Monooxygenase Ferredoxin Oxidoreductase. Biochemistry 2015; 54:5980-8. [PMID: 26309236 DOI: 10.1021/acs.biochem.5b00692] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 1.6 Å crystal structure of toluene 4-monooxygenase reductase T4moF is reported. The structure includes ferredoxin, flavin, and NADH binding domains. The position of the ferredoxin domain relative to the other two domains represents a new configuration for the iron-sulfur flavoprotein family. Close contacts between the C8 methyl group of FAD and [2Fe-2S] ligand Cys36-O represent a plausible pathway for electron transfer between the redox cofactors. Energy-minimized docking of NADH and calculation of hingelike motions between domains suggest how simple coordinated shifts of residues at the C-terminus of the enzyme could expose the N5 position of FAD for productive interaction with the nicotinamide ring. The domain configuration revealed by the T4moF structure provides an excellent steric and electrostatic match to the obligate electron acceptor, Rieske-type [2Fe-2S] ferredoxin T4moC. Protein-protein docking and energy minimization of the T4moFC complex indicate that T4moF [2Fe-2S] ligand Cys41 and T4moC [2Fe-2S] ligand His67, along with other electrostatic interactions between the protein partners, form the functional electron transfer interface.
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Affiliation(s)
- Justin F Acheson
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Hannah Moseson
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Brian G Fox
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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13
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Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies. ACTA ACUST UNITED AC 2015; 16:67-80. [PMID: 25854603 DOI: 10.1007/s10969-015-9198-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
Abstract
Vectors designed for protein production in Escherichia coli and by wheat germ cell-free translation were tested using 21 well-characterized eukaryotic proteins chosen to serve as controls within the context of a structural genomics pipeline. The controls were carried through cloning, small-scale expression trials, large-scale growth or synthesis, and purification. Successfully purified proteins were also subjected to either crystallization trials or (1)H-(15)N HSQC NMR analyses. Experiments evaluated: (1) the relative efficacy of restriction/ligation and recombinational cloning systems; (2) the value of maltose-binding protein (MBP) as a solubility enhancement tag; (3) the consequences of in vivo proteolysis of the MBP fusion as an alternative to post-purification proteolysis; (4) the effect of the level of LacI repressor on the yields of protein obtained from E. coli using autoinduction; (5) the consequences of removing the His tag from proteins produced by the cell-free system; and (6) the comparative performance of E. coli cells or wheat germ cell-free translation. Optimal promoter/repressor and fusion tag configurations for each expression system are discussed.
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14
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Bianchetti CM, Takasuka TE, Deutsch S, Udell HS, Yik EJ, Bergeman LF, Fox BG. Active site and laminarin binding in glycoside hydrolase family 55. J Biol Chem 2015; 290:11819-32. [PMID: 25752603 DOI: 10.1074/jbc.m114.623579] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 11/06/2022] Open
Abstract
The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.
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Affiliation(s)
- Christopher M Bianchetti
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, the Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, Wisconsin 54901
| | - Taichi E Takasuka
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, the Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Sam Deutsch
- the Joint Genome Institute, Walnut Creek, California 94598, and
| | - Hannah S Udell
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Eric J Yik
- the Department of Chemistry and Biochemistry, California State University-Fullerton, Fullerton, California 92831
| | - Lai F Bergeman
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Brian G Fox
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706,
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15
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Proteins interacting with cloning scars: a source of false positive protein-protein interactions. Sci Rep 2015; 5:8530. [PMID: 25704442 PMCID: PMC4336944 DOI: 10.1038/srep08530] [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: 01/14/2015] [Accepted: 01/23/2015] [Indexed: 01/10/2023] Open
Abstract
A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine "cloning scar" present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected.
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16
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Wang J, Xu R, Liu A. IRDL cloning: a one-tube, zero-background, easy-to-use, directional cloning method improves throughput in recombinant DNA preparation. PLoS One 2014; 9:e107907. [PMID: 25243603 PMCID: PMC4171505 DOI: 10.1371/journal.pone.0107907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022] Open
Abstract
Rapid and efficient construction of expression vectors and subsequent transformation are basic recombinant methods for the investigation of gene functionality. Although novel cloning methods have recently been developed, many laboratories worldwide continue to use traditional restriction digestion-ligation methods to construct expression vectors owing to financial constraints and the unavailability of appropriate vectors. We describe an improved restriction digestion-ligation (IRDL) cloning method that combines the advantage of directional cloning from double digestion-ligation with that of a low background observed by using a positive selection marker gene ccdB to facilitate digestion and ligation in a single tube. The IRDL cloning overcomes the time-consuming and laborious limits of traditional methods, thereby providing an easy-to-use, low-cost, and one-step strategy for directional cloning of target DNA fragments into an expression vector. As a proof-of-concept example, we developed two yeast vectors to demonstrate the feasibility and the flexibility of the IRDL cloning method. This method would provide an effective and easy-to-use system for gene cloning and functional genomics studies.
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Affiliation(s)
- Jiancai Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, People's Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Ronghua Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Aizhong Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Kunming, People's Republic of China
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17
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Biochemical properties and atomic resolution structure of a proteolytically processed β-mannanase from cellulolytic Streptomyces sp. SirexAA-E. PLoS One 2014; 9:e94166. [PMID: 24710170 PMCID: PMC3978015 DOI: 10.1371/journal.pone.0094166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/11/2014] [Indexed: 01/07/2023] Open
Abstract
β-Mannanase SACTE_2347 from cellulolytic Streptomyces sp. SirexAA-E is abundantly secreted into the culture medium during growth on cellulosic materials. The enzyme is composed of domains from the glycoside hydrolase family 5 (GH5), fibronectin type-III (Fn3), and carbohydrate binding module family 2 (CBM2). After secretion, the enzyme is proteolyzed into three different, catalytically active variants with masses of 53, 42 and 34 kDa corresponding to the intact protein, loss of the CBM2 domain, or loss of both the Fn3 and CBM2 domains. The three variants had identical N-termini starting with Ala51, and the positions of specific proteolytic reactions in the linker sequences separating the three domains were identified. To conduct biochemical and structural characterizations, the natural proteolytic variants were reproduced by cloning and heterologously expressed in Escherichia coli. Each SACTE_2347 variant hydrolyzed only β-1,4 mannosidic linkages, and also reacted with pure mannans containing partial galactosyl- and/or glucosyl substitutions. Examination of the X-ray crystal structure of the GH5 domain of SACTE_2347 suggests that two loops adjacent to the active site channel, which have differences in position and length relative to other closely related mannanases, play a role in producing the observed substrate selectivity.
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18
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Takasuka TE, Bianchetti CM, Tobimatsu Y, Bergeman LF, Ralph J, Fox BG. Structure-guided analysis of catalytic specificity of the abundantly secreted chitosanase SACTE_5457 from Streptomyces
sp. SirexAA-E. Proteins 2014; 82:1245-57. [DOI: 10.1002/prot.24491] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 01/22/2023]
Affiliation(s)
- Taichi E. Takasuka
- Department of Biochemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
- Great Lakes Bioenergy Research Center, College of Engineering; University of Wisconsin-Madison; Madison Wisconsin 53726
| | - Christopher M. Bianchetti
- Department of Biochemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
- Great Lakes Bioenergy Research Center, College of Engineering; University of Wisconsin-Madison; Madison Wisconsin 53726
| | - Yuki Tobimatsu
- Department of Biochemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
- Great Lakes Bioenergy Research Center, College of Engineering; University of Wisconsin-Madison; Madison Wisconsin 53726
| | - Lai F. Bergeman
- Department of Biochemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
- Great Lakes Bioenergy Research Center, College of Engineering; University of Wisconsin-Madison; Madison Wisconsin 53726
| | - John Ralph
- Department of Biochemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
- Great Lakes Bioenergy Research Center, College of Engineering; University of Wisconsin-Madison; Madison Wisconsin 53726
| | - Brian G. Fox
- Department of Biochemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
- Great Lakes Bioenergy Research Center, College of Engineering; University of Wisconsin-Madison; Madison Wisconsin 53726
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19
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Singh S, Chang A, Helmich KE, Bingman CA, Wrobel RL, Beebe ET, Makino SI, Aceti DJ, Dyer K, Hura GL, Sunkara M, Morris AJ, Phillips GN, Thorson JS. Structural and functional characterization of CalS11, a TDP-rhamnose 3'-O-methyltransferase involved in calicheamicin biosynthesis. ACS Chem Biol 2013; 8:1632-9. [PMID: 23662776 PMCID: PMC3875630 DOI: 10.1021/cb400068k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sugar methyltransferases (MTs) are an important class of tailoring enzymes that catalyze the transfer of a methyl group from S-adenosyl-l-methionine to sugar-based N-, C- and O-nucleophiles. While sugar N- and C-MTs involved in natural product biosynthesis have been found to act on sugar nucleotide substrates prior to a subsequent glycosyltransferase reaction, corresponding sugar O-methylation reactions studied thus far occur after the glycosyltransfer reaction. Herein we report the first in vitro characterization using (1)H-(13)C-gHSQC with isotopically labeled substrates and the X-ray structure determination at 1.55 Å resolution of the TDP-3'-O-rhamnose-methyltransferase CalS11 from Micromonospora echinospora. This study highlights a unique NMR-based methyltransferase assay, implicates CalS11 to be a metal- and general acid/base-dependent O-methyltransferase, and as a first crystal structure for a TDP-hexose-O-methyltransferase, presents a new template for mechanistic studies and/or engineering.
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Affiliation(s)
- Shanteri Singh
- Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, KY 40536-0596, USA
| | - Aram Chang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kate E. Helmich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Russel L. Wrobel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Emily T. Beebe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Shin-Ichi Makino
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David J. Aceti
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kevin Dyer
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Greg L. Hura
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Manjula Sunkara
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, KY 40536-0596, USA
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20
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Tryptophan-47 in the active site of Methylophaga sp. strain SK1 flavin-monooxygenase is important for hydride transfer. Arch Biochem Biophys 2013; 532:46-53. [PMID: 23357278 DOI: 10.1016/j.abb.2013.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/31/2012] [Accepted: 01/13/2013] [Indexed: 11/21/2022]
Abstract
Flavin-dependent monooxygenase (FMO) from Methylophaga sp. strain SK1 catalyzes the NADPH- and oxygen-dependent hydroxylation of a number of xenobiotics. Reduction of the flavin cofactor by NADPH is required for activation of molecular oxygen. The role of a conserved tryptophan at position 47 was probed by site-directed mutagenesis. FMOW47A resulted in an insoluble inactive protein; in contrast, FMOW47F was soluble and active. The spectrum of the flavin in the mutant enzyme was redshifted, indicating a change in the flavin environment. The kcat values for NADPH, trimethylamine, and methimazole, decreased 5-8-fold. Primary kinetic isotope effect values were higher, indicating that hydride transfer is more rate-limiting in the mutant enzyme. This is supported by a decrease in the rate constant for flavin reduction and in the solvent kinetic isotope effect values. Results from molecular dynamics simulations show reduced flexibility in active site residues and, in particular, the nicotinamide moiety of NADP+ in FMOW47F. This was supported by thermal denaturation experiments. Together, the data suggests that W47 plays a role in maintaining the overall protein flexibility that is required for conformational changes important in hydride transfer.
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21
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Chocklett SW, Sobrado P. Aspergillus fumigatus SidA is a highly specific ornithine hydroxylase with bound flavin cofactor. Biochemistry 2010; 49:6777-83. [PMID: 20614882 DOI: 10.1021/bi100291n] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferrichrome is a hydroxamate-containing siderophore produced by the pathogenic fungus Aspergillus fumigatus under iron-limiting conditions. This siderophore contains N(5)-hydroxylated l-ornithines essential for iron binding. A. fumigatus siderophore A (Af SidA) catalyzes the flavin- and NADPH-dependent hydroxylation of l-ornithine in ferrichrome biosynthesis. Af SidA was recombinantly expressed and purified as a soluble tetramer and is the first member of this class of flavin monooxygenases to be isolated with a bound flavin cofactor. The enzyme showed typical saturation kinetics with respect to l-ornithine while substrate inhibition was observed at high concentrations of NADPH and NADH. Increasing amounts of hydrogen peroxide were measured as a function of reduced nicotinamide coenzyme concentration, indicating that inhibition was caused by increased uncoupling. Af SidA is highly specific for its amino acid substrate, only hydroxylating l-ornithine. An 8-fold preference in the catalytic efficiency was determined for NADPH compared to NADH. In the absence of substrate, Af SidA can be reduced by NADPH, and a C4a-(hydro)peroxyflavin intermediate is observed. The decay of this intermediate is accelerated by l-ornithine binding. This intermediate was only stabilized by NADPH and not by NADH, suggesting a role for NADP(+) in the stabilization of intermediates in the reaction of Af SidA. NADP(+) is a competitive inhibitor with respect to NADPH, demonstrating that Af SidA forms a ternary complex with NADP(+) and l-ornithine during catalysis. The data suggest that Af SidA likely proceeds by a sequential kinetic mechanism.
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Affiliation(s)
- Samuel W Chocklett
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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22
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Bae E, Bitto E, Bingman CA, McCoy JG, Wesenberg GE, Phillips GN. Crystal structure of an eIF4G-like protein from Danio rerio. Proteins 2010; 78:1803-6. [PMID: 20229607 DOI: 10.1002/prot.22703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Euiyoung Bae
- Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Oppenheimer M, Pierce BS, Crawford JA, Ray K, Helm RF, Sobrado P. Recombinant expression, purification, and characterization of ThmD, the oxidoreductase component of tetrahydrofuran monooxygenase. Arch Biochem Biophys 2010; 496:123-31. [PMID: 20159007 DOI: 10.1016/j.abb.2010.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/09/2010] [Accepted: 02/10/2010] [Indexed: 11/29/2022]
Abstract
Tetrahydrofuran monooxygenase (Thm) catalyzes the NADH-and oxygen-dependent hydroxylation of tetrahydrofuran to 2-hydroxytetrahydrofuran. Thm is composed of a hydroxylase enzyme, a regulatory subunit, and an oxidoreductase named ThmD. ThmD was expressed in Escherichia coli as a fusion to maltose-binding protein (MBP) and isolated to homogeneity after removal of the MBP. Purified ThmD contains covalently bound FAD, [2Fe-2S] center, and was shown to use ferricyanide, cytochrome c, 2,6-dichloroindophenol, and to a lesser extent, oxygen as surrogate electron acceptors. ThmD displays 160-fold preference for NADH over NADPH and functions as a monomer. The flavin-binding domain of ThmD (ThmD-FD) was purified and characterized. ThmD-FD displayed similar activity as the full-length ThmD and showed a unique flavin spectrum with a major peak at 463nm and a small peak at 396 nm. Computational modeling and mutagenesis analyses suggest a novel three-dimensional fold or covalent flavin attachment in ThmD.
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