PoplarV1, Main, Exploration, bibRecord, 001897

Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity.

Identifieur interne : 001897 ( Main/Exploration ); précédent : 001896; suivant : 001898

Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity.

Auteurs : Aparajita Banerjee [États-Unis] ; Alyssa L. Preiser [États-Unis] ; Thomas D. Sharkey [États-Unis]

Source :

PloS one [ 1932-6203 ] ; 2016.

RBID : pubmed:27548482

Descripteurs français

English descriptors

KwdEn :
- Alanine (metabolism), Amino Acid Sequence (MeSH), Catalytic Domain (MeSH), Enzyme Inhibitors (chemistry), Feedback, Physiological (MeSH), Gene Expression (MeSH), Glycine (metabolism), Hemiterpenes (metabolism), Kinetics (MeSH), Ligands (MeSH), Models, Molecular (MeSH), Mutagenesis, Site-Directed (MeSH), Organophosphorus Compounds (metabolism), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (enzymology), Populus (genetics), Protein Binding (MeSH), Protein Engineering (MeSH), Protein Interaction Domains and Motifs (MeSH), Recombinant Proteins (genetics), Recombinant Proteins (metabolism), Sequence Alignment (MeSH), Sequence Homology, Amino Acid (MeSH), Substrate Specificity (MeSH), Thiamine Pyrophosphate (metabolism), Transferases (antagonists & inhibitors), Transferases (genetics), Transferases (metabolism).
MESH :
- chemical , antagonists & inhibitors : Transferases.
- chemical , chemistry : Enzyme Inhibitors.
- chemical , genetics : Plant Proteins, Recombinant Proteins, Transferases.
- chemical , metabolism : Alanine, Glycine, Hemiterpenes, Organophosphorus Compounds, Plant Proteins, Recombinant Proteins, Thiamine Pyrophosphate, Transferases.
- enzymology : Populus.
- genetics : Populus.
- Amino Acid Sequence, Catalytic Domain, Feedback, Physiological, Gene Expression, Kinetics, Ligands, Models, Molecular, Mutagenesis, Site-Directed, Protein Binding, Protein Engineering, Protein Interaction Domains and Motifs, Sequence Alignment, Sequence Homology, Amino Acid, Substrate Specificity.

Abstract

Deoxyxylulose 5-phosphate synthase (DXS), a thiamine diphosphate (ThDP) dependent enzyme, plays a regulatory role in the methylerythritol 4-phosphate (MEP) pathway. Isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the end products of this pathway, inhibit DXS by competing with ThDP. Feedback inhibition of DXS by IDP and DMADP constitutes a significant metabolic regulation of this pathway. The aim of this work was to experimentally test the effect of key residues of recombinant poplar DXS (PtDXS) in binding both ThDP and IDP. This work also described the engineering of PtDXS to improve the enzymatic activity by reducing its inhibition by IDP and DMADP. We have designed and tested modifications of PtDXS in an attempt to reduce inhibition by IDP. This could possibly be valuable by removing a feedback that limits the usefulness of the MEP pathway in biotechnological applications. Both ThDP and IDP use similar interactions for binding at the active site of the enzyme, however, ThDP being a larger molecule has more anchoring sites at the active site of the enzyme as compared to the inhibitors. A predicted enzyme structure was examined to find ligand-enzyme interactions, which are relatively more important for inhibitor-enzyme binding than ThDP-enzyme binding, followed by their modifications so that the binding of the inhibitors can be selectively affected compared to ThDP. Two alanine residues important for binding ThDP and the inhibitors were mutated to glycine. In two of the cases, both the IDP inhibition and the overall activity were increased. In another case, both the IDP inhibition and the overall activity were reduced. This provides proof of concept that it is possible to reduce the feedback from IDP on DXS activity.

DOI: 10.1371/journal.pone.0161534
PubMed: 27548482
PubMed Central: PMC4993486

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<series><title level="j">PloS one</title>
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<term>Amino Acid Sequence (MeSH)</term>
<term>Catalytic Domain (MeSH)</term>
<term>Enzyme Inhibitors (chemistry)</term>
<term>Feedback, Physiological (MeSH)</term>
<term>Gene Expression (MeSH)</term>
<term>Glycine (metabolism)</term>
<term>Hemiterpenes (metabolism)</term>
<term>Kinetics (MeSH)</term>
<term>Ligands (MeSH)</term>
<term>Models, Molecular (MeSH)</term>
<term>Mutagenesis, Site-Directed (MeSH)</term>
<term>Organophosphorus Compounds (metabolism)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Populus (enzymology)</term>
<term>Populus (genetics)</term>
<term>Protein Binding (MeSH)</term>
<term>Protein Engineering (MeSH)</term>
<term>Protein Interaction Domains and Motifs (MeSH)</term>
<term>Recombinant Proteins (genetics)</term>
<term>Recombinant Proteins (metabolism)</term>
<term>Sequence Alignment (MeSH)</term>
<term>Sequence Homology, Amino Acid (MeSH)</term>
<term>Substrate Specificity (MeSH)</term>
<term>Thiamine Pyrophosphate (metabolism)</term>
<term>Transferases (antagonists & inhibitors)</term>
<term>Transferases (genetics)</term>
<term>Transferases (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Alanine (métabolisme)</term>
<term>Alignement de séquences (MeSH)</term>
<term>Antienzymes (composition chimique)</term>
<term>Cinétique (MeSH)</term>
<term>Composés organiques du phosphore (métabolisme)</term>
<term>Diphosphate de thiamine (métabolisme)</term>
<term>Domaine catalytique (MeSH)</term>
<term>Expression des gènes (MeSH)</term>
<term>Glycine (métabolisme)</term>
<term>Hémiterpènes (métabolisme)</term>
<term>Ingénierie des protéines (MeSH)</term>
<term>Liaison aux protéines (MeSH)</term>
<term>Ligands (MeSH)</term>
<term>Modèles moléculaires (MeSH)</term>
<term>Motifs et domaines d'intéraction protéique (MeSH)</term>
<term>Mutagenèse dirigée (MeSH)</term>
<term>Populus (enzymologie)</term>
<term>Populus (génétique)</term>
<term>Protéines recombinantes (génétique)</term>
<term>Protéines recombinantes (métabolisme)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Rétrocontrôle physiologique (MeSH)</term>
<term>Similitude de séquences d'acides aminés (MeSH)</term>
<term>Spécificité du substrat (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Transferases (antagonistes et inhibiteurs)</term>
<term>Transferases (génétique)</term>
<term>Transferases (métabolisme)</term>
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</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Enzyme Inhibitors</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term>
<term>Recombinant Proteins</term>
<term>Transferases</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Alanine</term>
<term>Glycine</term>
<term>Hemiterpenes</term>
<term>Organophosphorus Compounds</term>
<term>Plant Proteins</term>
<term>Recombinant Proteins</term>
<term>Thiamine Pyrophosphate</term>
<term>Transferases</term>
</keywords>
<keywords scheme="MESH" qualifier="antagonistes et inhibiteurs" xml:lang="fr"><term>Transferases</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Antienzymes</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term>
<term>Protéines recombinantes</term>
<term>Protéines végétales</term>
<term>Transferases</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Alanine</term>
<term>Composés organiques du phosphore</term>
<term>Diphosphate de thiamine</term>
<term>Glycine</term>
<term>Hémiterpènes</term>
<term>Protéines recombinantes</term>
<term>Protéines végétales</term>
<term>Transferases</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Catalytic Domain</term>
<term>Feedback, Physiological</term>
<term>Gene Expression</term>
<term>Kinetics</term>
<term>Ligands</term>
<term>Models, Molecular</term>
<term>Mutagenesis, Site-Directed</term>
<term>Protein Binding</term>
<term>Protein Engineering</term>
<term>Protein Interaction Domains and Motifs</term>
<term>Sequence Alignment</term>
<term>Sequence Homology, Amino Acid</term>
<term>Substrate Specificity</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term>
<term>Cinétique</term>
<term>Domaine catalytique</term>
<term>Expression des gènes</term>
<term>Ingénierie des protéines</term>
<term>Liaison aux protéines</term>
<term>Ligands</term>
<term>Modèles moléculaires</term>
<term>Motifs et domaines d'intéraction protéique</term>
<term>Mutagenèse dirigée</term>
<term>Rétrocontrôle physiologique</term>
<term>Similitude de séquences d'acides aminés</term>
<term>Spécificité du substrat</term>
<term>Séquence d'acides aminés</term>
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<front><div type="abstract" xml:lang="en">Deoxyxylulose 5-phosphate synthase (DXS), a thiamine diphosphate (ThDP) dependent enzyme, plays a regulatory role in the methylerythritol 4-phosphate (MEP) pathway. Isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the end products of this pathway, inhibit DXS by competing with ThDP. Feedback inhibition of DXS by IDP and DMADP constitutes a significant metabolic regulation of this pathway. The aim of this work was to experimentally test the effect of key residues of recombinant poplar DXS (PtDXS) in binding both ThDP and IDP. This work also described the engineering of PtDXS to improve the enzymatic activity by reducing its inhibition by IDP and DMADP. We have designed and tested modifications of PtDXS in an attempt to reduce inhibition by IDP. This could possibly be valuable by removing a feedback that limits the usefulness of the MEP pathway in biotechnological applications. Both ThDP and IDP use similar interactions for binding at the active site of the enzyme, however, ThDP being a larger molecule has more anchoring sites at the active site of the enzyme as compared to the inhibitors. A predicted enzyme structure was examined to find ligand-enzyme interactions, which are relatively more important for inhibitor-enzyme binding than ThDP-enzyme binding, followed by their modifications so that the binding of the inhibitors can be selectively affected compared to ThDP. Two alanine residues important for binding ThDP and the inhibitors were mutated to glycine. In two of the cases, both the IDP inhibition and the overall activity were increased. In another case, both the IDP inhibition and the overall activity were reduced. This provides proof of concept that it is possible to reduce the feedback from IDP on DXS activity. </div>
</front>
</TEI>
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<DateCompleted><Year>2017</Year>
<Month>08</Month>
<Day>01</Day>
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<ArticleTitle>Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity.</ArticleTitle>
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<Abstract><AbstractText>Deoxyxylulose 5-phosphate synthase (DXS), a thiamine diphosphate (ThDP) dependent enzyme, plays a regulatory role in the methylerythritol 4-phosphate (MEP) pathway. Isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the end products of this pathway, inhibit DXS by competing with ThDP. Feedback inhibition of DXS by IDP and DMADP constitutes a significant metabolic regulation of this pathway. The aim of this work was to experimentally test the effect of key residues of recombinant poplar DXS (PtDXS) in binding both ThDP and IDP. This work also described the engineering of PtDXS to improve the enzymatic activity by reducing its inhibition by IDP and DMADP. We have designed and tested modifications of PtDXS in an attempt to reduce inhibition by IDP. This could possibly be valuable by removing a feedback that limits the usefulness of the MEP pathway in biotechnological applications. Both ThDP and IDP use similar interactions for binding at the active site of the enzyme, however, ThDP being a larger molecule has more anchoring sites at the active site of the enzyme as compared to the inhibitors. A predicted enzyme structure was examined to find ligand-enzyme interactions, which are relatively more important for inhibitor-enzyme binding than ThDP-enzyme binding, followed by their modifications so that the binding of the inhibitors can be selectively affected compared to ThDP. Two alanine residues important for binding ThDP and the inhibitors were mutated to glycine. In two of the cases, both the IDP inhibition and the overall activity were increased. In another case, both the IDP inhibition and the overall activity were reduced. This provides proof of concept that it is possible to reduce the feedback from IDP on DXS activity. </AbstractText>
</Abstract>
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<ForeName>Aparajita</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Preiser</LastName>
<ForeName>Alyssa L</ForeName>
<Initials>AL</Initials>
<AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Sharkey</LastName>
<ForeName>Thomas D</ForeName>
<Initials>TD</Initials>
<Identifier Source="ORCID">http://orcid.org/0000-0002-4423-3223</Identifier>
<AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America.</Affiliation>
</AffiliationInfo>
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<Chemical><RegistryNumber>0</RegistryNumber>
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<Chemical><RegistryNumber>358-72-5</RegistryNumber>
<NameOfSubstance UI="C043060">3,3-dimethylallyl pyrophosphate</NameOfSubstance>
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<Chemical><RegistryNumber>EC 2.-</RegistryNumber>
<NameOfSubstance UI="D014166">Transferases</NameOfSubstance>
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<NameOfSubstance UI="C109461">deoxyxylulose-5-phosphate synthase</NameOfSubstance>
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<CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>PLoS One. 2016 Oct 13;11(10 ):e0165028</RefSource>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000409" MajorTopicYN="N">Alanine</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020134" MajorTopicYN="N">Catalytic Domain</DescriptorName>
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<MeshHeading><DescriptorName UI="D004791" MajorTopicYN="N">Enzyme Inhibitors</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D025461" MajorTopicYN="N">Feedback, Physiological</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015870" MajorTopicYN="N">Gene Expression</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005998" MajorTopicYN="N">Glycine</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D045782" MajorTopicYN="N">Hemiterpenes</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D007700" MajorTopicYN="N">Kinetics</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008024" MajorTopicYN="N">Ligands</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016297" MajorTopicYN="N">Mutagenesis, Site-Directed</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009943" MajorTopicYN="N">Organophosphorus Compounds</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
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   |texte=   Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity.
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Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity.

Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity.

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