Metabolic role of aldehyde dehydrogenases in <i>Pseudomonas putida</i> KT2440
Notice bibliographique
Résumé
Pseudomonas is one of the most complex bacterial genera and is currently the genus of Gram‐negative bacteria with the largest number of species. Pseudomonas include a metabolically versatile group of organisms that are known to occupy numerous ecological niches. Pseudomonas putida is a non‐pathogenic, soil bacterium with a flexible and robust metabolism. P. putida KT2440 possesses a large genome (5,564 genes), lending to its adaptability to varying environments. The repertoire of P. putida genes, which are substantially conserved among different strains, is populated with sophisticated regulatory systems that are foundational to respond and adapt to diverse environments. P. putida KT2440 possesses an unexpected high number (32) of aldehyde dehydrogenase ( aldh ) genes (by comparison humans possess only 19 different aldh genes), but only a few of these ALDHs have been characterized. To obtain insights about the metabolic role performed by each one of the 32 ALDHs found in P. putida KT2440, the genomic neighborhoods of aldh genes were analyzed and compared with neighborhoods in other Pseudomonas strains. Thus, phylogenetic analyses and genomic context data of aldh genes were used to predict the functional role of ALDHs in P. putida KT2440. Our results show that ALDHs belong to 24 different ALDH families. Among them, we found ALDH families 3, 4, 5, 6, 7, 9, 10, 11, 14, 18, 21, 26, 27, and 28, as well as 10 additional families not named yet by the ALDH nomenclature committee (ALDH28 family is also called cd07129 by NCBI’s Conserved Domain Database (CDD) < https://www.ncbi.nlm.nih.gov/cdd >). These ALDHs seem to play several metabolic roles such as glyceraldehyde 3‐phosphate and succinate semialdehyde metabolism, betaine aldehyde and proline synthesis, beta alanine, propanoate and amino acids catabolism, among others. It is interesting to note that P. putida KT2440 possesses several ALDH isoenzymes that belong to the same family. Three ALDH proteins from P. putida KT2440 belong to the ALDH28 family, while each of the families 5, 6, 14, 26, 27 and 29 is represented by two ALDH proteins (ALDH29 family is also called cd07100 by NCBI’s CDD). This diversity, as well as the genomic context of the corresponding a ldh genes, suggest that different ALDH isoenzymes within a same ALDH family are used to challenge different metabolic conditions. These results show that the metabolic role of a particular ALDH protein is dependent of both, kinetic properties of the enzyme as well as the proteins that are coexpressed with it (operon). Therefore, a specific ALDH family can participate in more than one metabolic pathway, thus contributing to the ability of this bacterium to survive and adapt to varying environments. Support or Funding Information Supported by DGAPA‐UNAM grant IN218819. Linear representation of Pseudomonas putida KT2440 chromosome 1, mapping 32 aldehyde dehydrogenase ( aldh ) gene loci. ALDH families are indicated between parenthesis. Figure 1
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».