On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w

Organisms must either synthesize or assimilate essential organic compounds to survive. The homocysteine synthase Met15 has been considered essential for inorganic sulfur assimilation in yeast since its discovery in the 1970s. As a result, MET15 has served as a genetic marker for hundreds of experiments that play a foundational role in eukaryote genetics and systems biology. Nevertheless, we demonstrate here through structural and evolutionary modeling, in vitro kinetic assays, and genetic complementation, that an alternative homocysteine synthase encoded by the previously uncharacterized gene YLL058W enables cells lacking Met15 to assimilate enough inorganic sulfur for survival and proliferation. These cells however fail to grow in patches or liquid cultures unless provided with exogenous methionine or other organosulfurs. We show that this growth failure, which has historically justified the status of MET15 as a classic auxotrophic marker, is largely explained by toxic accumulation of the gas hydrogen sulfide because of a metabolic bottleneck. When patched or cultured with a hydrogen sulfide chelator, and when propagated as colony grids, cells without Met15 assimilate inorganic sulfur and grow, and cells with Met15 achieve even higher yields. Thus, Met15 is not essential for inorganic sulfur assimilation in yeast. Instead, MET15 is the first example of a yeast gene whose loss conditionally prevents growth in a manner that depends on local gas exchange. Our results have broad implications for investigations of sulfur metabolism, including studies of stress response, methionine restriction, and aging. More generally, our findings illustrate how unappreciated experimental variables can obfuscate biological discovery.

Translational control by diverse RNA folds that recognize the metabolite preQ1

Typical paradigms of translational regulation utilize proteins, whereas riboswitches are economical, RNA-based elements that govern gene expression without protein partners. Present in all domains of life, riboswitches are commonly located in the 5´-untranslated regions of bacterial mRNAs where they establish feedback loops that respond to cellular levels of a specific small-molecule effector. Here we present the novel crystal structure of the recently discovered preQ1-III (class 3) riboswitch at 2.85 Å resolution. The 101-nucleotide switch features an internal loop pseudoknot (iPK) that coaxially stacks upon flanking helices P2 and P3. PreQ1(7-aminomethyl-7-deazaguanine) – the last soluble intermediate in the biosynthesis of the hypermodified tRNA base queuosine (Scheme I) – binds to form a major groove base triple of the form U·preQ1·C that utilizes highly conserved pyrimidine bases that help define this riboswitch class. This mode of effector binding involves non-canonical Watson-Crick pairing reminiscent of the phylogenetically unrelated preQ1-II (class 2) riboswitch. Remarkably, both riboswitch classes utilize dual U·A-U base triples that stack against the ligand. The respective nine-nucleotide motifs and their preQ1ligands superimpose with an rmsd of 0.4 Å; the class 2 and 3 structures are otherwise unrelated. The class 3 preQ1binding pocket also includes contributions from junctions that connect the P2-iPK-P3 coaxial stack with perpendicularly positioned helix P4. Of special interest is the observation that P4 can form a hairpin-loop pseudoknot (hPK) with the ribosome binding site (RBS) of the mRNA, suggesting a mode of ligand-dependent RBS sequestration. Biochemical experiments describing the preQ1dependence of hPK formation will be presented, as well as a comparison to known, translational class 1 and 2 preQ1riboswitch structures [1-3]. Implications for bacterial translational control will be discussed based on this diverse riboswitch family.

Hexim-1 modulates androgen receptor and the TGF-β signaling during the progression of prostate cancer

BACKGROUND

Androgen and TGF-β signaling are important components during the progression of prostate cancer. However, whether common molecular events participate in the activation of these signaling pathways are less understood.

METHOD

Hexim 1 expression was detected by immunohistochemistry of human tissue microarrays and TRAMP mouse models. The in vivo significance of Hexim-1 was established by crossing the TRAMP mouse model of prostate cancer with Hexim-1 heterozygous mice. TRAMP C2 cell line was also modified to delete one copy of Hexim-1 gene to generate TRAMP-C2-Hexim-1+/- cell lines.

RESULTS

In this report, we observed that Hexim-1 protein expression is absent in normal prostate but highly expressed in adenocarcinoma of the prostate and a characteristic sub-cellular distribution among normal, benign hyperplasia, and adenocarcinoma of the prostate. Heterozygosity of the Hexim-1 gene in the prostate cancer mice model and the TRAMP-C2 cell line, leads to increased Cdk9-dependent serine phosphorylation on protein targets such as the androgen receptor (AR) and the TGF-β-dependent downstream transcription factors, such as the SMAD proteins.

CONCLUSION

Our results suggest that changes in the Hexim-1 protein expression and cellular distribution significantly influences the AR activation and the TGF-β signaling. Thus, Hexim-1 is likely to play a significant role in prostate cancer progression.