The oligomeric state of the proteolipid subunit of V-ATPase from Saccharomyces cerevisiae was studied using hemagglutinine (HA) epitope-tag. Like with several other highly hydrophobic proteins, the proteolipid tends to aggregate in the presence of sodium dodecyl sulfate (SDS). We observed that the oligomeric state of the proteolipid predetermined its tendency for aggregation. Recently we discovered a novel V-ATPase subunit, denoted as M16 for the mammalian enzyme and Vma10p for the yeast enzyme, that is homologous to the b subunit of the membrane sector of F-ATPases. It is assumed that the structure of Vma10p resembles that of subunit b which is basically two anti parallel helices. We mutated the VMA10 gene to change charges on the protein in helices and to introduce helix braking instead of helix forming amino acids. The functionality of the mutated VMA10 was analyzed by growing the transformed yeast cells on a YPD medium buffered at pH 7.5. Two inactive site-directed mutants we used for obtaining second-site suppressors. Mutagenesis with EMS was utilized to get an equal chance of obtaining intra and extragene second-site suppressors. To our surprise the number of colonies that grew at pH 7.5 was too large to account for mutations in V-ATPase subunits. Apparently, mutations that are situated in genes that do not encode V-ATPase subunits could reverse the phenotype of V-ATPase null mutations resulting in growth at pH 7.5. The large number of colonies that grew at pH 7.5 after EMS treatment suggest a big complex with multiple subunits as a target for mutagenesis. The observed phenomenon is very intriguing. If the responsible protein complex is identified, it may shed light on an important and novel cell biology subject.