Figure 6.

The RSC protein complex (right) together with the related SWI/SNF complex (left) exhibit intricate homologous relationships between complexes' components. SWI/SNF and RSC complexes share 3 common proteins (ARP7, ARP9, RTT102). Additional three genes from each complex are paralogs (dashed lines), suggesting series of duplications (this includes a WGD pair RSC6-SNF12). For these bi-complex paralogs, it is very likely that the pre-duplication/ancestral forms of these genes were participating in both complexes, and the duplication event allowed paralogs to assume more specific roles in either complex. Zinc-cluster domain containing RSC3 and RSC30 are paralogs found in RSC complexes in equal proportions [43] and are known to interact physically, forming a stable heteromeric complex [21]. Despite operating as a heterodimer (possibly within the RSC complex as well), the two genes have different functions, with only RSC3 being an essential gene. The intra-complex paralog pair originated at the WGD event. At a given time, both proteins can be found in the complex, hence increase the subunit count by one above the initial complex, given that the ancestral interaction was probably a homomeric one. RSC1 and RSC2 (WGD paralogs), associate with the complex in a mutually exclusive manner [47] (confirmed by a low spoke value of 2.1 compared to average 5.0 for other subunits). Strains deficient in either RSC1 or RSC2 do not display significant growth deficiency, while synthetic lethality of paralogs suggests a certain degree of function redundancy [47]. A similar, but non-identical function of the two paralogs is revealed by differences in phenotypes of yeast strains with RSC1 (growth deficiency in hydroxyurea) or RSC2 deletions (temperature sensitive, [47]). Both complexes are required for certain functions such as proper expression of mid-late sporulation specific genes (e.g. spore wall formation), yet distinctly required, and specialized, for other operations [48]. The two module variants can be seen as a remarkable example of subfunctionalization.