HOG pathway-dependent repression of genes, and multiple functional modes of Hog1. Each plot shows the average fold induction (in log2 scale) of novel gene modules (A) or known targets of TFs (B) in wild type (WT) and seven HOG pathway mutants exposed to 0.5 M KCl. Black/white coloring indicates average fold induction above/below 0.1. (A) The novel modules Hog1A, Hog1B, and Hog1/Ca (the Hog1C and Ssk2/22 modules [data not shown] are similar to Hog1B in this view). (B) The known target genes of Ste12 (KSS1, TEC1, FUS1, FUS3, MSG5, KAR4, CLN1, PGU1), Hog1 (HOR2, GRE2, STL1, ENA1, GLR1, GPD1, HAL1, CHA1, AHP1, YGR043C, YGR052W (reserved name FMP48), YML131W; Hohmann 2002), and Msn2/4 (Rep et al. 2000). Expression of the novel modules Hog1B and Hog1/Ca (A, middle and bottom) increases in the absence of Hog1. Although the whole Hog1-dependent inhibition response is known to be regulated by Ste12, one can clearly see that these novel modules differ significantly from the Ste12 targets (B, top), indicating existence of Hog1-dependent in spite of Ste12-independent inhibition. The known Hog1/Msn1/Sko1 and Msn2/4 targets (B, middle and bottom) have distinct expression pattern (KS-test P-value < 10−5): The Msn1/Hot1/Sko1 targets have higher expression in the ssk1ste11 and ssk1sho1 mutants compared to hog1 and pbs2 mutants, indicating that Hog1 can be activated also by a third additional input. In contrast, the Msn2/4 targets have a similar expression pattern in all four of these mutants, indicating that Hog1 is dependent on the two upstream branches of the HOG pathway. Surprisingly, the novel modules' expression pattern (A) also suggests dependency on the two HOG branches. One can clearly see that two of these modules (Hog1B and Hog1/Ca) differ significantly from the known Msn2/4 targets (the distinction between Msn2/4 and the third module Hog1A is discussed in Fig. 5). Taken together, this suggests that Hog1 has two distinct functional modes that involve a different combination of transcription factors. An extended version of the novel modules appears in Supplement C.
