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Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
Pyridoxal 5’-phosphate or PLP is a cofactor derived from B(6) vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B(6) transporters, are still to be identified in ma...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997740/ https://www.ncbi.nlm.nih.gov/pubmed/36729913 http://dx.doi.org/10.1099/mgen.0.000926 |
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author | Denise, Rémi Babor, Jill Gerlt, John A. de Crécy-Lagard, Valérie |
author_facet | Denise, Rémi Babor, Jill Gerlt, John A. de Crécy-Lagard, Valérie |
author_sort | Denise, Rémi |
collection | PubMed |
description | Pyridoxal 5’-phosphate or PLP is a cofactor derived from B(6) vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B(6) transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis . Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B(6) vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come. |
format | Online Article Text |
id | pubmed-9997740 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-99977402023-03-10 Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes Denise, Rémi Babor, Jill Gerlt, John A. de Crécy-Lagard, Valérie Microb Genom Research Articles Pyridoxal 5’-phosphate or PLP is a cofactor derived from B(6) vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B(6) transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis . Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B(6) vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come. Microbiology Society 2023-02-02 /pmc/articles/PMC9997740/ /pubmed/36729913 http://dx.doi.org/10.1099/mgen.0.000926 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution. |
spellingShingle | Research Articles Denise, Rémi Babor, Jill Gerlt, John A. de Crécy-Lagard, Valérie Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes |
title | Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes |
title_full | Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes |
title_fullStr | Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes |
title_full_unstemmed | Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes |
title_short | Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes |
title_sort | pyridoxal 5’-phosphate synthesis and salvage in bacteria and archaea: predicting pathway variant distributions and holes |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997740/ https://www.ncbi.nlm.nih.gov/pubmed/36729913 http://dx.doi.org/10.1099/mgen.0.000926 |
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