Studies On Saccharomyces Cerevisiae RNA Polymerase II Subunit Rpb7 And Its Eukaryotic Orthologs

Abstract

Saccharomyces cerevisiae is an excellent experimental model organism to study various biological processes owing to its versatile genetics, biochemistry, and standard laboratory conditions. S. cerevisiae shows distinct biological responses under nutritional starvation conditions. S. cerevisiae undergoes dimorphic transition from a unicellular yeast form to a multicellular pseudohyphae (Gimeno et al., 1992) under nitrogen starvation, but in the complete absence of a fermentable carbon source, it undergoes gametogenesis called sporulation (Mitchell, 1994). While the signal transduction cascades and regulatory controls under nutritional starvation conditions are studied to great extent, the role of S. cerevisiae core RNA polymerase II (pol II) is not much understood. S. cerevisiae core RNA pol II consists of 12 subunits (Woychik and Hampsey, 2002), which is organized into a ten-subunit core and the Rpb4/7 subcomplex (Edwards et al., 1991). Rpb4/7 subcomplex is known to play important roles in stress survival (Choder 2004; Sampath and Sadhale, 2005.). S. cerevisiae rpb4 null diploid strains show reduced sporulation levels but exhibits a predisposition to pseudohyphal morphology (Pillai et al., 2003). Overexpression of Rpb7 partially rescues some of these defects (Sharma et al., 1999; Sheffer et al., 2001). Rpb7 is a highly conserved protein but Rpb4 is the least conserved amongst all RNA pol II subunits at the sequence level. Rpb4 and Rpb7 also affect different cellular functions, which are not directly dependent on each other. (a) Relative levels of RNA pol II subunits Rpb4 and Rpb7 differentially affect starvation response in Saccharomyces cerevisiae S. cerevisiae rpb4 null diploid strains show reduced sporulation levels as compared to wild type but exhibits pseudohyphal predisposition. Overexpression of RPB7 partially rescues the sporulation defect but results in an exaggeration of the pseudohyphae phenotype. We generated S. cerevisiae strains expressing different levels of Rpb4 and Rpb7 proteins in the same strains and analyzed their effect on sporulation and pseudohyphal morphology. We observed that sporulation is dependent on Rpb4 because sporulation level gradually increases with an increase in the Rpb4 protein level in the strain. Rpb7 reduces sporulation level but enhances pseudohyphal exaggeration in a dose-dependent manner. Rpb4 is dominant over Rpb7 in both the starvation responses because strain expressing an equimolar ratio of Rpb4 and Rpb7 protein exhibits RPB4+ phenotypes. (b) Domainal organization of Saccharomyces cerevisiae Rpb7 orthologs reflects functional conservation Rpb7 orthologs are known in eukaryotes and archaebacteria. The primary structure of Rpb7 is conserved. We chose Rpb7 orthologs from Candida albicans, Schizosaccharomyces pombe and Homo sapiens sapiens to investigate whether Rpb7 orthologs are also functionally conserved. We observed that all the orthologs tested are functionally conserved because they can complement the absence of RPB7 in S. cerevisiae. However, we uncovered functional differences amongst Rpb7 orthologs with respect to its function in rpb4 null strain and ess1 ts strain. Furthermore, we made N and C-terminal chimeric RPB7 constructs from these orthologs with S. cerevisiae Rpb7. These chimeras also can replace ScRpb7 in S. cerevisiae. However, functional differences were observed with each chimera pair in rpb4 null strain and ess1 ts strain, showing that the N and C-terminal domains of Rpb7 protein can be genetically dissected. The genetic observation on the domainal organization of Rpb7 orthologs is strengthened by the crystal structure of Rpb7 (Armache et al., 2005), which shows that Rpb7 is structurally organized into an N terminal RNP domain and a C terminal OB fold domain. (c) The Rpb7 subunit of Candida albicans RNA polymerase II induces lectin-mediated flocculation in Saccharomyces cerevisiae The Rpb7 ortholog of C. albicans is a conserved functional ortholog of ScRpb7. We observed that CaRpb7 induces Ca2+-dependent flocculation and agar-invasive growth in S. cerevisiae. CaRpb7 overexpression induces very high transcript levels of FLO1 and FLO11. We believe that the observed flocculation and agar-invasive phenotypes are due to Flo1 and Flo11 respectively, because Flo1 and Flo11 contribute mainly to cell-cell adhesion while Flo11 contributes mainly to cell-substrate adhesion (Verstrepen and Klis, 2006; Lo et al., 1998; Guo et al., 2000). Pathway analysis revealed that CaRpb7-induced flocculation is dependent on Mss11 transcriptional activator. Two-hybrid analysis revealed that CaRpb7 does not physically interact with transcriptional repressors known to repress FLO gene transcription, however genetic analysis revealed that CaRpb7 is epistatic to the repressor Sfl1. Rpb7 orthologs possess conserved domains with potential RNA binding ability (Orlicky et al., 1999) and ScRpb7 is known to play in mRNA stability (Lotan et al., 2007). The possibility of CaRpb7 specifically affecting the stability of FLO gene transcripts is being pursued.