Metabolic role of aldehyde dehydrogenases in Pseudomonas putida KT2440

Abstract

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 aldh 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 InformationSupported 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