Redirecting linear hydrocarbon metabolism toward polyhydroxyalkanoate biosynthesis

TL;DR

This study shows how a bacteria strain can convert specific hydrocarbons into a biopolymer called PHA, especially under nitrogen-limited conditions.

Contribution

The discovery of a novel alkane monooxygenase fusion enzyme and its role in directing carbon toward PHA synthesis is presented.

Findings

The AlkB enzyme oxidizes n-octane and n-decane into octanoate and decanoate, entering β-oxidation and the glyoxylate shunt.

A phaZ-deficient mutant accumulates PHA up to 75% of cell dry weight under nitrogen limitation.

13C-isotopic labeling revealed unexpected C10 monomers from C8 substrates, possibly from de novo fatty acid synthesis.

Abstract

This study explores how Pseudomonas putida EM2-4 metabolizes linear alkanes after acquiring an integrative and conjugative element (ICE) encoding a novel alkane monooxygenase (AlkB). This AlkB enzyme is a fusion of a hydroxylase and a fatty acid desaturase, exhibiting a narrow substrate range limited to n-octane and n-decane. The oxidation of these hydrocarbons yields octanoate and decanoate, respectively, which then enter the β-oxidation pathway and the glyoxylate shunt. Under nitrogen-limiting conditions, excess carbon is redirected toward polyhydroxyalkanoate (PHA) synthesis, a phenomenon particularly pronounced in a phaZ-deficient mutant unable to depolymeraze PHA, leading to up 75% of cell dry weight. Analysis of the PHAs monomer composition revealed variations with the carbon source. Additionally, 13C-isotopic labeling uncovered a minor but unexpected fraction of C10 monomers from C8 substrates, potentially arised from gluconeogenesis followed by the de novo synthesis of fatty acids. Proteomic analyses showed that the carbon source influences the activation of metabolic pathways, correlating with the observed variations in PHAs monomer composition.

The online version contains supplementary material available at 10.1186/s12934-025-02914-7.

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