The biogenesis of mammalian ATP synthase is complex process believed to proceed via several modules. It starts with the formation of F1 catalytic part, which is in the later steps connected with the membranous subcomplex. The final phase is represented by incorporation of the two mtDNA-encoded subunits Fo-a and A6L. However, little is known about the position of two newly described Fo accessory subunits DAPIT (also termed Usmg5) and MLQ (also known as c14orf2) in the assembly scheme and about their role in regulation of ATP synthase biogenesis. To resolve this, we have utilised several model systems, namely rho0 cells lacking mtDNA and thus both subunits Fo-a and A6L, cells harbouring 9205delTA microdeletion, which results in the absence of the subunit Fo-a, HEK293 cells with knockdown of DAPIT protein and HEK293 cells with knockout of MLQ protein and followed the assembly state of ATP synthase among them. Contrary to previously reported data, we observed normal levels of assembled ATP synthase in DAPIT knockdown and MLQ knockout cells. Our results indicate that lack of DAPIT protein leads to the assembly of more labile, but complete and functional holoenzyme. Absence of either Fo-a alone or Fo-a and A6L results into the normal levels of structurally altered, labile, and ~60 kDa smaller vestigial enzyme complex, which also lacks DAPIT and MLQ. This complex retains the ATP hydrolytic activity but is unable to synthesize ATP. Cells with the MLQ knockout presented with the phenotype similar to the lack of Fo-a: normal content of smaller and labile complex. In the absence of MLQ, vestigial ATP synthase did not contain also subunits Fo-a and A6L. This complex also retained ATP hydrolytic activity, while its phosphorylating capacity was affected. In all the cell lines tested, the individual subunits seemed to be associated only with assembled ATP synthase complex, indicating that once subunits dissociate from the complex, they are degraded in the cell. This hypothesis is supported by the fact, that in the cells lacking subunit MLQ the biosynthesis of both mtDNA-encoded subunits Fo-a and A6L is normal, but they are degraded at faster pace than the rest of the complex. Based on our data, we conclude that MLQ and Fo-a closely associate and their incorporation into the enzyme complex depends on each another. On the contrary, DAPIT protein seems to be incorporated at the very last step and its presence stabilises the holoenzyme.
