Novel deep branching Cu-containing membrane-bound monooxygenases: distribution and function

The key enzyme of the aerobic methane oxidation is the particulate methane monooxygenase (pMMO) pMMOs are members of the great family of Cu-containing membrane-bound monooxygenases (CuMMO). Genes of the pMMO operon can occur in multiple copies within the genome of methanotrophic bacteria. Some of them encode pMMO isoenzymes with alternative functions. A new isoenzyme (pXMO) has been recently found in some alpha- and gamma-proteobacterial methanotrophs. pxmA sequences of this isoenzyme do not cluster within groups of characterized pmoA sequences but within the environmental group (M84_P105) that belongs to the distantly related intermediate CuMMO (iCuMMO). To analyze the distribution of pxmA sequences in methanotrophic pure cultures and nature primers were designed that target several iCuMMO groups (including M84_P105). The pxmA could be detected in several strains of the methylotrophic genera Methylomonas, Methylobacter and Methylosarcina. Additionally, it could be shown that pxmA sequences are widespread and numerous in different environment. Almost all iCuMMO groups are not represented by pure cultures. Hence, little sequence information is available which makes the study of the iCuMMOs difficult. A magnetic capture hybridization method (MCH) was established to gain more sequence information of the iCuMMOs. MCH avoids the use of specific primers and may provide long target sequences and information about operon structures of the iCuMMOs. The physiological functions of the iCuMMOs are unknown. Due to a phylogenetic relationship of pxmA sequences to sequences of alkane oxidizers we suggested that they might be involved in alkane degradation, too. However, incubation experiments of pure cultures and environmental indicate that the analyzed iCuMMOs are not involved in alkane degradation. Pure culture incubations indicate that the pxmA of the environmental group M84_P105 might be involved in methane oxidation. But further studies need to be performed to confirm this hypothesis. The physiological function of the other iCuMMO groups remains still unknown. iCuMMOs were underestimated for a long time but this study shows that are widely distributed and may play an important role global element cycles. Methanotrophic bacteria has been believed to be obligate but facultative methanotrophs has been found among the type II methanotrophs that grow on substrates with carbon-carbon bounds like acetate, pyruvate, succinate, malate and ethanol. In this study we could show that type II methanotrophs play a role in the degradation of short chained alkanes in rice field soils. If they use the alkanes directly or if they use metabolic products provided by other bacteria needs to be analyzed. But these findings show that the restricted role of the methanotrophs to certain substrates and specific functions needs to be expended