Activation of Haa1 and War1 transcription factors by differential binding of weak acid anions in Saccharomyces cerevisiae.

In Saccharomyces cerevisiae, Haa1 and War1 transcription factors are involved in cellular adaptation against hydrophilic weak acids and lipophilic weak acids, respectively. However, it is unclear how these transcription factors are differentially activated depending on the identity of the weak acid. Using a field-effect transistor (FET)-type biosensor based on carbon nanofibers, in the present study we demonstrate that Haa1 and War1 directly bind to various weak acid anions with different affinities. Haa1 is most sensitive to acetate, followed by lactate, whereas War1 is most sensitive to benzoate, followed by sorbate, reflecting their differential activation during weak acid stresses. We show that DNA binding by Haa1 is induced in the presence of acetic acid and that the N-terminal Zn-binding domain is essential for this activity. Acetate binds to the N-terminal 150-residue region, and the transcriptional activation domain is located between amino acid residues 230 and 483. Our data suggest that acetate binding converts an inactive Haa1 to the active form, which is capable of DNA binding and transcriptional activation.

Role of CK2-dependent phosphorylation of Ifh1 and Crf1 in transcriptional regulation of ribosomal protein genes in Saccharomyces cerevisiae.

In Saccharomyces cerevisiae, Fhl1 is involved in the regulation of ribosomal protein (RP) genes through interaction with either its coactivator Ifh1 or corepressor Crf1, depending on nutrient conditions. Interaction of Fhl1 with Ifh1 or Crf1 is achieved through a forkhead-associated (FHA) domain of Fhl1, which binds to forkhead-binding (FHB) domains of Ifh1 and Crf1. Here, we demonstrate that CK2-dependent phosphorylation of T681 and T348 residues, located in the FHB domains of Ifh1 and Crf1, respectively, provides binding sites for the FHA domain of Fhl1. Cells expressing Ifh1(T681A) mutant showed reduced association of Ifh1 at the RP gene promoters and decreased levels of RP gene transcripts, thereby reducing the growth rate. On the other hand, cells expressing Crf1(T348A) showed a defect in repressing RP gene transcription upon inhibition of target of rapamycin complex 1 (TORC1) by rapamycin treatment. Taken together, these findings suggest the mechanisms by which CK2-dependent recruitment of Ifh1 and Crf1 at the RP gene promoters governs the transcription of RP genes.

Deubiquitinase USP1 enhances CCAAT/enhancer-binding protein beta (C/EBPß) stability and accelerates adipogenesis and lipid accumulation.

Dysregulation of the ubiquitin-proteasome system has been implicated in the pathogenesis of several metabolic disorders, including obesity, diabetes, and non-alcoholic fatty liver disease; however, the mechanisms controlling pathogenic metabolic disorders remain unclear. Transcription factor CCAAT/enhancer binding protein beta (C/EBPß) regulates adipogenic genes. The study showed that the expression level of C/EBPß is post-translationally regulated by the deubiquitinase ubiquitin-specific protease 1 (USP1) and that USP1 expression is remarkably upregulated during adipocyte differentiation and in the adipose tissue of mice fed a high-fat diet (HFD). We found that USP1 directly interacts with C/EBPß. Knock-down of USP1 decreased C/EBPß protein stability and increased its ubiquitination. Overexpression of USP1 regulates its protein stability and ubiquitination, whereas catalytic mutant of USP1 had no effect on them. It suggests that USP1 directly deubiquitinases C/EBPß and increases the protein expression, leading to adipogenesis and lipid accumulation. Notably, the USP1-specific inhibitor ML323-originally developed to sensitize cancer cells to DNA-damaging agents-decreased adipocyte differentiation and lipid accumulation in 3T3-L1 cells without cytotoxicity. Oral gavage of ML323 was administered to HFD-fed mice, which showed weight loss and improvement in insulin and glucose sensitivity. Both fat mass and adipocyte size in white adipose tissues were significantly reduced by ML323 treatment, which also reduced the expression of genes involved in adipogenesis and inflammatory responses. ML323 also reduced lipid accumulation, hepatic triglycerides, free fatty acids, and macrophage infiltration in the livers of HFD-fed mice. Taken together, we suggest that USP1 plays an important role in adipogenesis by regulating C/EBPß ubiquitination, and USP1-specific inhibitor ML323 is a potential treatment option and further study by ML323 is needed for clinical application for metabolic disorders.

Ablation of the deubiquitinase USP15 ameliorates nonalcoholic fatty liver disease and nonalcoholic steatohepatitis.

Nonalcoholic fatty liver disease (NAFLD) occurs due to the accumulation of fat in the liver, leading to fatal liver diseases such as nonalcoholic steatohepatitis (NASH) and cirrhosis. Elucidation of the molecular mechanisms underlying NAFLD is critical for its prevention and therapy. Here, we observed that deubiquitinase USP15 expression was upregulated in the livers of mice fed a high-fat diet (HFD) and liver biopsies of patients with NAFLD or NASH. USP15 interacts with lipid-accumulating proteins such as FABPs and perilipins to reduce ubiquitination and increase their protein stability. Furthermore, the severity of NAFLD induced by an HFD and NASH induced by a fructose/palmitate/cholesterol/trans-fat (FPC) diet was significantly ameliorated in hepatocyte-specific USP15 knockout mice. Thus, our findings reveal an unrecognized function of USP15 in the lipid accumulation of livers, which exacerbates NAFLD to NASH by overriding nutrients and inducing inflammation. Therefore, targeting USP15 can be used in the prevention and treatment of NAFLD and NASH.

Dynamics of bacteriophage R17 probed with a long-lifetime Ru(II) metal-ligand complex.

The metal-ligand complex, [Ru(2,2'-bipyridine)(2)(4,4'-dicarboxy-2,2'-bipyridine)](2+) (RuBDc), was used as a spectroscopic probe for studying macromolecular dynamics. RuBDc is a very photostable probe that possesses favorable photophysical properties including long lifetime, high quantum yield, large Stokes' shift, and highly polarized emission. To further show the usefulness of this luminophore for probing macromolecular dynamics, we examined the intensity and anisotropy decays of RuBDc when conjugated to R17 bacteriophage using frequency-domain fluorometry with a blue light-emitting diode (LED) as the modulated light source. The intensity decays were best fit by a sum of two exponentials, and we obtained a longer mean lifetime at 4 degrees C ( = 491.8 ns) as compared to that at 25 degrees C ( = 435.1 ns). The anisotropy decay data showed a single rotational correlation time, which is typical for a spherical molecule, and the results showed a longer rotational correlation time at 4 degrees C (2,574.9 ns) than at 25 degrees C (2,070.1 ns). The use of RuBDc enabled us to measure the rotational correlation time up to several microseconds. These results indicate that RuBDc has significant potential for studying hydrodynamics of biological macromolecules.

Rim15-dependent activation of Hsf1 and Msn2/4 transcription factors by direct phosphorylation in Saccharomyces cerevisiae.

Rim15 kinase, a downstream effector of PKA and TORC1 signaling pathways, initiates the quiescent program upon nutrient starvation via induction of genes whose expression depends on transcription factors Msn2, Msn4, and Gis1. Here, we demonstrate that Rim15 also induces expression of Hsf1 target genes upon glucose depletion by both transcriptional activation and stabilization of the transcripts. Rim15 phosphorylates Hsf1 in vitro, suggesting that Rim15 might directly activate Hsf1. In addition, Igo1 and Igo2, Rim15 substrate proteins involved in mRNA stabilization, regulate mRNA levels of Hsf1 target genes. We also show that Rim15 can phosphorylate Msn2, but not Gis1, in vitro, implying different mechanisms for the activation of these transcription factors.