Pseudomonas putida IOFA1 transcriptome profiling reveals a metabolic pathway involved in formaldehyde degradation

Abstract

Some strains belonging to Pseudomonas putida have been found to degrade formaldehyde, making them promising methylotrophic bacteria in the treatment of environmental formaldehyde. However, the pathway involved in formaldehyde degradation of P. putida has not been extensively investigated. P. putida IOFA1, a strain isolated from the deep-sea sediments of the Indian Ocean, was found to be extremely tolerant of formaldehyde (up to 10mM), efficiently degrading formaldehyde. In this study, the transcriptome profiles of the IOFA1 strain at different stages of formaldehyde degradation were characterized. A total of 709 genes were found to be significantly altered during formaldehyde degradation. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis showed that methanol metabolism, protein synthesis, and material transportation were highly enriched during formaldehyde degradation. The expression pattern of key methanol metabolism genes, which may be responsible for formaldehyde degradation, was investigated further with the quantitative real-time chain reaction (qRT-PCR) method. Our results showed that the IOFA1 strain may adopt a metabolic strategy of formaldehyde degradation different from other reported methylotrophic microorganisms. Therefore, our study presents a novel insight into the mechanism of formaldehyde degradation, which may help in engineering P. putida strains with a greater ability of degrading formaldehyde.