Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis

Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets with a methyl thioether group (–SCH3). Members of two of the four known subgroups of MTTases have been characterized, typified by MiaB, which modifies N6-isopentenyladenosine (i6A) to 2-methylthio-N6-isopentenyladenosine (ms2i6A) in tRNA, and RimO, which modifies a specific aspartate residue in ribosomal protein S12. In this work, we have characterized the two MTTases encoded by Bacillus subtilis 168 and find that, consistent with bioinformatic predictions, ymcB is required for ms2i6A formation (MiaB activity), and yqeV is required for modification of N6-threonylcarbamoyladenosine (t6A) to 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A) in tRNA. The enzyme responsible for the latter activity belongs to a third MTTase subgroup, no member of which has previously been characterized. We performed domain-swapping experiments between YmcB and YqeV to narrow down the protein domain(s) responsible for distinguishing i6A from t6A and found that the C-terminal TRAM domain, putatively involved with RNA binding, is likely not involved with this discrimination. Finally, we performed a computational analysis to identify candidate residues outside the TRAM domain that may be involved with substrate recognition. These residues represent interesting targets for further analysis

Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis

Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets with a methyl thioether group (–SCH3). Members of two of the four known subgroups of MTTases have been characterized, typified by MiaB, which modifies N6-isopentenyladenosine (i6A) to 2-methylthio-N6-isopentenyladenosine (ms2i6A) in tRNA, and RimO, which modifies a specific aspartate residue in ribosomal protein S12. In this work, we have characterized the two MTTases encoded by Bacillus subtilis 168 and find that, consistent with bioinformatic predictions, ymcB is required for ms2i6A formation (MiaB activity), and yqeV is required for modification of N6-threonylcarbamoyladenosine (t6A) to 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A) in tRNA. The enzyme responsible for the latter activity belongs to a third MTTase subgroup, no member of which has previously been characterized. We performed domain-swapping experiments between YmcB and YqeV to narrow down the protein domain(s) responsible for distinguishing i6A from t6A and found that the C-terminal TRAM domain, putatively involved with RNA binding, is likely not involved with this discrimination. Finally, we performed a computational analysis to identify candidate residues outside the TRAM domain that may be involved with substrate recognition. These residues represent interesting targets for further analysis

Insertion de soufre en biologie par voie radicalaire. Etude des méthylthiotransférases

One of the chemically most challenging problems in enzymology is the functionalization of non-reactive C–H bonds. Such reactions require specialized cofactors as heme, Fe-µ-oxo or vitamin B12. In 2001, special Fe-S centers able to bind S-Adenosylmethionine (SAM) have been shown to activate non-reactive C-H bonds toward subsequent functionalization. Enzymes containing this new cofactor constitute a super-family called “Radical SAM”. Methylthiotransferases (MTTases) belong to the “Radical SAM” super-family and catalyse the insertion of a methylthio group (-SCH3) in C-H bonds. By doing in vitro and in vivo experiments, we were able to classify them into three groups. The first class, (RimO) catalyses the formation of β-methylthio-aspartate 89 on the ribosomal protein S12 (β-ms-D89-S12) whereas the two others (MiaB and MtaB/eMtaB) respectively catalyse the thiomethylation of the nucleosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) and 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) present in some tRNA. Our studies have shown that, in vitro, MTTases catalyse the insertion of a SCH3 group in a catalytic way suggesting entirely new radical sulfur insertion mechanisms.Un des problèmes majeurs en enzymologie est la fonctionnalisation de liaisons C-H peu réactives. Ces réactions nécessitent des cofacteurs spécialisés tels que l'hème, des Fer-oxo ou encore la vitamine B12. En 2001, il a été montré que des centres Fe-S particuliers liant la S-Adénosyle méthionine (SAM) pouvaient activer des liaisons C-H non réactives. Les enzymes utilisant ce cofacteur constituent une super-famille appelée « Radical SAM ». Les thiométhyltransférases (MTTases) sont des enzymes « Radical SAM » qui catalysent l'insertion d'un groupe thiométhyle (-SCH3) dans des liaisons C-H non réactives. Par des expériences in vivo et in vitro, nous avons montré qu'on pouvait les regrouper en trois classes. La première classe (RimO) catalyse la formation du β-thiométhylaspartate 89 sur la protéine ribosomale S12 (β-ms-D89-S12) alors que les deux dernières (MiaB et MtaB/eMtaB) catalysent respectivement la thiométhylation des nucléosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) et 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) de certains ARNts. L'étude in vitro du mécanisme de ces enzymes a permis de démontrer que les MTTases catalysent l'insertion d'un groupement -SCH3 de façon catalytique invalidant l'hypothèse généralement retenue dans la littérature que le soufre inséré dérive de la destruction d'un centre Fe-S

Insertion de soufre en biologie par voie radicalaire. Etude des méthylthiotransférases

One of the chemically most challenging problems in enzymology is the functionalization of non-reactive C–H bonds. Such reactions require specialized cofactors as heme, Fe-µ-oxo or vitamin B12. In 2001, special Fe-S centers able to bind S-Adenosylmethionine (SAM) have been shown to activate non-reactive C-H bonds toward subsequent functionalization. Enzymes containing this new cofactor constitute a super-family called “Radical SAM”. Methylthiotransferases (MTTases) belong to the “Radical SAM” super-family and catalyse the insertion of a methylthio group (-SCH3) in C-H bonds. By doing in vitro and in vivo experiments, we were able to classify them into three groups. The first class, (RimO) catalyses the formation of β-methylthio-aspartate 89 on the ribosomal protein S12 (β-ms-D89-S12) whereas the two others (MiaB and MtaB/eMtaB) respectively catalyse the thiomethylation of the nucleosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) and 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) present in some tRNA. Our studies have shown that, in vitro, MTTases catalyse the insertion of a SCH3 group in a catalytic way suggesting entirely new radical sulfur insertion mechanisms.Un des problèmes majeurs en enzymologie est la fonctionnalisation de liaisons C-H peu réactives. Ces réactions nécessitent des cofacteurs spécialisés tels que l'hème, des Fer-oxo ou encore la vitamine B12. En 2001, il a été montré que des centres Fe-S particuliers liant la S-Adénosyle méthionine (SAM) pouvaient activer des liaisons C-H non réactives. Les enzymes utilisant ce cofacteur constituent une super-famille appelée « Radical SAM ». Les thiométhyltransférases (MTTases) sont des enzymes « Radical SAM » qui catalysent l'insertion d'un groupe thiométhyle (-SCH3) dans des liaisons C-H non réactives. Par des expériences in vivo et in vitro, nous avons montré qu'on pouvait les regrouper en trois classes. La première classe (RimO) catalyse la formation du β-thiométhylaspartate 89 sur la protéine ribosomale S12 (β-ms-D89-S12) alors que les deux dernières (MiaB et MtaB/eMtaB) catalysent respectivement la thiométhylation des nucléosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) et 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) de certains ARNts. L'étude in vitro du mécanisme de ces enzymes a permis de démontrer que les MTTases catalysent l'insertion d'un groupement -SCH3 de façon catalytique invalidant l'hypothèse généralement retenue dans la littérature que le soufre inséré dérive de la destruction d'un centre Fe-S

Biological radical sulfur insertion. A study of methylthiotransferases.

Un des problèmes majeurs en enzymologie est la fonctionnalisation de liaisons C-H peu réactives. Ces réactions nécessitent des cofacteurs spécialisés tels que l'hème, des Fer-oxo ou encore la vitamine B12. En 2001, il a été montré que des centres Fe-S particuliers liant la S-Adénosyle méthionine (SAM) pouvaient activer des liaisons C-H non réactives. Les enzymes utilisant ce cofacteur constituent une super-famille appelée « Radical SAM ». Les thiométhyltransférases (MTTases) sont des enzymes « Radical SAM » qui catalysent l'insertion d'un groupe thiométhyle (-SCH3) dans des liaisons C-H non réactives. Par des expériences in vivo et in vitro, nous avons montré qu'on pouvait les regrouper en trois classes. La première classe (RimO) catalyse la formation du β-thiométhylaspartate 89 sur la protéine ribosomale S12 (β-ms-D89-S12) alors que les deux dernières (MiaB et MtaB/eMtaB) catalysent respectivement la thiométhylation des nucléosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) et 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) de certains ARNts. L'étude in vitro du mécanisme de ces enzymes a permis de démontrer que les MTTases catalysent l'insertion d'un groupement -SCH3 de façon catalytique invalidant l'hypothèse généralement retenue dans la littérature que le soufre inséré dérive de la destruction d'un centre Fe-S.One of the chemically most challenging problems in enzymology is the functionalization of non-reactive C–H bonds. Such reactions require specialized cofactors as heme, Fe-µ-oxo or vitamin B12. In 2001, special Fe-S centers able to bind S-Adenosylmethionine (SAM) have been shown to activate non-reactive C-H bonds toward subsequent functionalization. Enzymes containing this new cofactor constitute a super-family called “Radical SAM”. Methylthiotransferases (MTTases) belong to the “Radical SAM” super-family and catalyse the insertion of a methylthio group (-SCH3) in C-H bonds. By doing in vitro and in vivo experiments, we were able to classify them into three groups. The first class, (RimO) catalyses the formation of β-methylthio-aspartate 89 on the ribosomal protein S12 (β-ms-D89-S12) whereas the two others (MiaB and MtaB/eMtaB) respectively catalyse the thiomethylation of the nucleosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) and 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) present in some tRNA. Our studies have shown that, in vitro, MTTases catalyse the insertion of a SCH3 group in a catalytic way suggesting entirely new radical sulfur insertion mechanisms

Insertion de soufre en biologie par voie radicalaire. Etude des méthylthiotransférases

One of the chemically most challenging problems in enzymology is the functionalization of non-reactive C–H bonds. Such reactions require specialized cofactors as heme, Fe-µ-oxo or vitamin B12. In 2001, special Fe-S centers able to bind S-Adenosylmethionine (SAM) have been shown to activate non-reactive C-H bonds toward subsequent functionalization. Enzymes containing this new cofactor constitute a super-family called “Radical SAM”. Methylthiotransferases (MTTases) belong to the “Radical SAM” super-family and catalyse the insertion of a methylthio group (-SCH3) in C-H bonds. By doing in vitro and in vivo experiments, we were able to classify them into three groups. The first class, (RimO) catalyses the formation of β-methylthio-aspartate 89 on the ribosomal protein S12 (β-ms-D89-S12) whereas the two others (MiaB and MtaB/eMtaB) respectively catalyse the thiomethylation of the nucleosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) and 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) present in some tRNA. Our studies have shown that, in vitro, MTTases catalyse the insertion of a SCH3 group in a catalytic way suggesting entirely new radical sulfur insertion mechanisms.Un des problèmes majeurs en enzymologie est la fonctionnalisation de liaisons C-H peu réactives. Ces réactions nécessitent des cofacteurs spécialisés tels que l'hème, des Fer-oxo ou encore la vitamine B12. En 2001, il a été montré que des centres Fe-S particuliers liant la S-Adénosyle méthionine (SAM) pouvaient activer des liaisons C-H non réactives. Les enzymes utilisant ce cofacteur constituent une super-famille appelée « Radical SAM ». Les thiométhyltransférases (MTTases) sont des enzymes « Radical SAM » qui catalysent l'insertion d'un groupe thiométhyle (-SCH3) dans des liaisons C-H non réactives. Par des expériences in vivo et in vitro, nous avons montré qu'on pouvait les regrouper en trois classes. La première classe (RimO) catalyse la formation du β-thiométhylaspartate 89 sur la protéine ribosomale S12 (β-ms-D89-S12) alors que les deux dernières (MiaB et MtaB/eMtaB) catalysent respectivement la thiométhylation des nucléosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) et 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) de certains ARNts. L'étude in vitro du mécanisme de ces enzymes a permis de démontrer que les MTTases catalysent l'insertion d'un groupement -SCH3 de façon catalytique invalidant l'hypothèse généralement retenue dans la littérature que le soufre inséré dérive de la destruction d'un centre Fe-S

Insertion de soufre en biologie par voie radicalaire. Etude des méthylthiotransférases

Un des problèmes majeurs en enzymologie est la fonctionnalisation de liaisons C-H peu réactives. Ces réactions nécessitent des cofacteurs spécialisés tels que l'hème, des Fer-oxo ou encore la vitamine B12. En 2001, il a été montré que des centres Fe-S particuliers liant la S-Adénosyle méthionine (SAM) pouvaient activer des liaisons C-H non réactives. Les enzymes utilisant ce cofacteur constituent une super-famille appelée Radical SAM . Les thiométhyltransférases (MTTases) sont des enzymes Radical SAM qui catalysent l'insertion d'un groupe thiométhyle (-SCH3) dans des liaisons C-H non réactives. Par des expériences in vivo et in vitro, nous avons montré qu'on pouvait les regrouper en trois classes. La première classe (RimO) catalyse la formation du b-thiométhylaspartate 89 sur la protéine ribosomale S12 (b-ms-D89-S12) alors que les deux dernières (MiaB et MtaB/eMtaB) catalysent respectivement la thiométhylation des nucléosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) et 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) de certains ARNts. L'étude in vitro du mécanisme de ces enzymes a permis de démontrer que les MTTases catalysent l'insertion d'un groupement -SCH3 de façon catalytique invalidant l'hypothèse généralement retenue dans la littérature que le soufre inséré dérive de la destruction d'un centre Fe-S.One of the chemically most challenging problems in enzymology is the functionalization of non-reactive C H bonds. Such reactions require specialized cofactors as heme, Fe- -oxo or vitamin B12. In 2001, special Fe-S centers able to bind S-Adenosylmethionine (SAM) have been shown to activate non-reactive C-H bonds toward subsequent functionalization. Enzymes containing this new cofactor constitute a super-family called Radical SAM . Methylthiotransferases (MTTases) belong to the Radical SAM super-family and catalyse the insertion of a methylthio group (-SCH3) in C-H bonds. By doing in vitro and in vivo experiments, we were able to classify them into three groups. The first class, (RimO) catalyses the formation of b-methylthio-aspartate 89 on the ribosomal protein S12 (b-ms-D89-S12) whereas the two others (MiaB and MtaB/eMtaB) respectively catalyse the thiomethylation of the nucleosides 2-methylthio-N6-isopentenyladenosine 37 (ms2i6A-37) and 2-methylthio-N6-threoninecarbamoyl adenosine 37 (ms2t6A-37) present in some tRNA. Our studies have shown that, in vitro, MTTases catalyse the insertion of a SCH3 group in a catalytic way suggesting entirely new radical sulfur insertion mechanisms.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF