Essentiality of the <i>Escherichia coli</i> YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme
Enzymes carrying Iron-Sulfur (Fe-S) clusters perform many important cellular functions and their biogenesis require complex protein machinery. In mitochondria, the IBA57 protein is essential and promotes assembly of [4Fe-4S] clusters and their insertion into acceptor proteins. YgfZ is the bacterial...
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MDPI AG
2023-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/5/4728 |
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| author | Torben Lund Maria Yohanna Kulkova Rosa Jersie-Christensen Tove Atlung |
| author_facet | Torben Lund Maria Yohanna Kulkova Rosa Jersie-Christensen Tove Atlung |
| author_sort | Torben Lund |
| collection | DOAJ |
| description | Enzymes carrying Iron-Sulfur (Fe-S) clusters perform many important cellular functions and their biogenesis require complex protein machinery. In mitochondria, the IBA57 protein is essential and promotes assembly of [4Fe-4S] clusters and their insertion into acceptor proteins. YgfZ is the bacterial homologue of IBA57 but its precise role in Fe-S cluster metabolism is uncharacterized. YgfZ is needed for activity of the radical S-adenosyl methionine [4Fe-4S] cluster enzyme MiaB which thiomethylates some tRNAs. The growth of cells lacking YgfZ is compromised especially at low temperature. The RimO enzyme is homologous to MiaB and thiomethylates a conserved aspartic acid in ribosomal protein S12. To quantitate thiomethylation by RimO, we developed a bottom-up LC-MS<sup>2</sup> analysis of total cell extracts. We show here that the in vivo activity of RimO is very low in the absence of YgfZ and independent of growth temperature. We discuss these results in relation to the hypotheses relating to the role of the auxiliary 4Fe-4S cluster in the Radical SAM enzymes that make Carbon-Sulfur bonds. |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T07:22:27Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-46390d8691974c4e9ae7bbbd5ed30d2d2023-11-17T07:52:35ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-03-01245472810.3390/ijms24054728Essentiality of the <i>Escherichia coli</i> YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO EnzymeTorben Lund0Maria Yohanna Kulkova1Rosa Jersie-Christensen2Tove Atlung3Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, DenmarkDepartment of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, DenmarkDepartment of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, DenmarkDepartment of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, DenmarkEnzymes carrying Iron-Sulfur (Fe-S) clusters perform many important cellular functions and their biogenesis require complex protein machinery. In mitochondria, the IBA57 protein is essential and promotes assembly of [4Fe-4S] clusters and their insertion into acceptor proteins. YgfZ is the bacterial homologue of IBA57 but its precise role in Fe-S cluster metabolism is uncharacterized. YgfZ is needed for activity of the radical S-adenosyl methionine [4Fe-4S] cluster enzyme MiaB which thiomethylates some tRNAs. The growth of cells lacking YgfZ is compromised especially at low temperature. The RimO enzyme is homologous to MiaB and thiomethylates a conserved aspartic acid in ribosomal protein S12. To quantitate thiomethylation by RimO, we developed a bottom-up LC-MS<sup>2</sup> analysis of total cell extracts. We show here that the in vivo activity of RimO is very low in the absence of YgfZ and independent of growth temperature. We discuss these results in relation to the hypotheses relating to the role of the auxiliary 4Fe-4S cluster in the Radical SAM enzymes that make Carbon-Sulfur bonds.https://www.mdpi.com/1422-0067/24/5/4728S12 D884Fe-4S clusterRadical SAMbottom-up proteomicstargeted LC-MS<sup>2</sup> |
| spellingShingle | Torben Lund Maria Yohanna Kulkova Rosa Jersie-Christensen Tove Atlung Essentiality of the <i>Escherichia coli</i> YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme International Journal of Molecular Sciences S12 D88 4Fe-4S cluster Radical SAM bottom-up proteomics targeted LC-MS<sup>2</sup> |
| title | Essentiality of the <i>Escherichia coli</i> YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme |
| title_full | Essentiality of the <i>Escherichia coli</i> YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme |
| title_fullStr | Essentiality of the <i>Escherichia coli</i> YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme |
| title_full_unstemmed | Essentiality of the <i>Escherichia coli</i> YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme |
| title_short | Essentiality of the <i>Escherichia coli</i> YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme |
| title_sort | essentiality of the i escherichia coli i ygfz protein for the in vivo thiomethylation of ribosomal protein s12 by the rimo enzyme |
| topic | S12 D88 4Fe-4S cluster Radical SAM bottom-up proteomics targeted LC-MS<sup>2</sup> |
| url | https://www.mdpi.com/1422-0067/24/5/4728 |
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