Hot off the presses! Dec 11 Mol Cell

The Dec 11 issue of the Mol Cell is now up on Pubget (About Mol Cell): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Reverse Transcribing the Code for Chromosome Stability
  - Mol Cell 36(5):715-719 (2009)
  The linearity of eukaryotic chromosomes presents challenges to cells, as the presence of DNA "ends" poses problems for the DNA replication machinery and the cell's damage response systems. This year's Nobel Prize in Physiology or Medicine recognized groundbreaking studies establishing the telomere field as a crucial area of biomedical research.
• Signaling Motifs and Weber's Law
  - Mol Cell 36(5):724-727 (2009)
  New experimental and theoretical studies reported by Uri Alon, Marc Kirschner, and colleagues in this issue of Molecular Cell suggest that Weber's law of sensory perception may apply to a number of cell signaling processes.
• Evolving Protein Stability through Genetic Selection
  - Mol Cell 36(5):730-731 (2009)
  In this issue of Molecular Cell, Foit et al. (2009) probe cellular protein folding using a split β-lactamase approach for evolving protein stability in the absence of any requirement for function.
• Checkpoint Mec-tivation Comes in Many Flavors
  - Mol Cell 36(5):734-735 (2009)
  In this issue of Molecular Cell, Navadgi-Patil and Burgers show that the budding yeast Mec1 kinase is activated by DNA damage through two distinct Ddc1-mediated mechanisms during G1 and G2 phases of the cell cycle.
• The Unstructured C-Terminal Tail of the 9-1-1 Clamp Subunit Ddc1 Activates Mec1/ATR via Two Distinct Mechanisms
  - Mol Cell 36(5):743-753 (2009)
  DNA damage checkpoint pathways operate to prevent cell-cycle progression in response to DNA damage and replication stress. In S. cerevisiae, Mec1-Ddc2 (human ATR-ATRIP) is the principal checkpoint protein kinase. Biochemical studies have identified two factors, the 9-1-1 checkpoint clamp and the Dpb11/TopBP1 replication protein, as potential activators of Mec1/ATR. Here, we show that G1 phase checkpoint activation of Mec1 is achieved by the Ddc1 subunit of 9-1-1, while Dpb11 is dispensable. However, in G2, 9-1-1 activates Mec1 by two distinct mechanisms. One mechanism involves direct activation of Mec1 by Ddc1, while the second proceeds by Dpb11 recruitment mediated through Ddc1 T602 phosphorylation. Two aromatic residues, W352 and W544, localized to two widely separated, conserved motifs of Ddc1, are essential for Mec1 activation in vitro and checkpoint function in G1. Remarkably, small peptides that fuse the two tryptophan-containing motifs together are proficient in! activating Mec1.
• Rrp17p Is a Eukaryotic Exonuclease Required for 5′ End Processing of Pre-60S Ribosomal RNA
  - Mol Cell 36(5):768-781 (2009)
  Ribosomal processing requires a series of endo- and exonucleolytic steps for the production of mature ribosomes, of which most have been described. To ensure ribosome synthesis, 3′ end formation of rRNA uses multiple nucleases acting in parallel; however, a similar parallel mechanism had not been described for 5′ end maturation. Here, we identify Rrp17p as a previously unidentified 5′–3′ exonuclease essential for ribosome biogenesis, functioning with Rat1p in a parallel processing pathway analogous to that of 3′ end formation. Rrp17p is required for efficient exonuclease digestion of the mature 5′ ends of 5.8SS and 25S rRNAs, contains a catalytic domain close to its N terminus, and is highly conserved among higher eukaryotes, being a member of a family of exonucleases. We show that Rrp17p binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery, and provide evidence for physical and functional links between late 60S subu! nit processing and export.
• Ubiquitinated Proteins Activate the Proteasome by Binding to Usp14/Ubp6, which Causes 20S Gate Opening
  - Mol Cell 36(5):794-804 (2009)
  In eukaryotic cells, ubiquitination of proteins leads to their degradation by the 26S proteasome. We tested if the ubiquitin (Ub) chain also regulates the proteasome's capacity for proteolysis. After incubation with polyubiquitinated proteins, 26S proteasomes hydrolyzed peptides and proteins 2- to 7-fold faster. Ub conjugates enhanced peptide hydrolysis by stimulating gate opening in the 20S proteasome. This stimulation was seen when this gate was closed or transiently open, but not maximally open. Gate opening requires conjugate association with Usp14/Ubp6 and also occurs if Ub aldehyde occupies this isopeptidase's active site. No stimulation was observed with 26S from Ubp6Δ mutants, but this effect was restored upon addition of Usp14/Ubp6 (even an inactive Ubp6). The stimulation of gate opening by Ub conjugates through Usp14/Ubp6 requires nucleotide binding to the gate-regulatory ATPases. This activation enhances the selectivity of the 26S proteasome for ubiquitinat! ed proteins and links their deubiquitination to their degradation.
• The Pseudoactive Site of ILK Is Essential for Its Binding to α-Parvin and Localization to Focal Adhesions
  - Mol Cell 36(5):819-830 (2009)
  Integrin-linked kinase (ILK) plays a pivotal role in connecting transmembrane receptor integrin to the actin cytoskeleton and thereby regulating diverse cell-adhesion-dependent processes. The kinase domain (KD) of ILK is indispensable for its function, but the underlying molecular basis remains enigmatic. Here we present the crystal structure of the ILK KD bound to its cytoskeletal regulator, the C-terminal calponin homology domain of α-parvin. While maintaining a canonical kinase fold, the ILK KD displays a striking pseudoactive site conformation. We show that rather than performing the kinase function, this conformation specifically recognizes α-parvin for promoting effective assembly of ILK into focal adhesions. The α-parvin-bound ILK KD can simultaneously engage integrin β cytoplasmic tails. These results thus define ILK as a distinct pseudokinase that mechanically couples integrin and α-parvin for mediating cell adhesion. They also highlight functional divers! ity of the kinase fold and its "active" site in mediating many biological processes.
• Hydroxyurea Induces Hydroxyl Radical-Mediated Cell Death in Escherichia coli
  - Mol Cell 36(5):845-860 (2009)
  Hydroxyurea (HU) specifically inhibits class I ribonucleotide reductase (RNR), depleting dNTP pools and leading to replication fork arrest. Although HU inhibition of RNR is well recognized, the mechanism by which it leads to cell death remains unknown. To investigate the mechanism of HU-induced cell death, we used a systems-level approach to determine the genomic and physiological responses of E. coli to HU treatment. Our results suggest a model by which HU treatment rapidly induces a set of protective responses to manage genomic instability. Continued HU stress activates iron uptake and toxins MazF and RelE, whose activity causes the synthesis of incompletely translated proteins and stimulation of envelope stress responses. These effects alter the properties of one of the cell's terminal cytochrome oxidases, causing an increase in superoxide production. The increased superoxide production, together with the increased iron uptake, fuels the formation of hydroxyl radica! ls that contribute to HU-induced cell death.
• Evidence that Fold-Change, and Not Absolute Level, of β-Catenin Dictates Wnt Signaling
  - Mol Cell 36(5):872-884 (2009)
  In response to Wnt stimulation, β-catenin accumulates and activates target genes. Using modeling and experimental analysis, we found that the level of β-catenin is sensitive to perturbations in the pathway, such that cellular variation would be expected to alter the signaling outcome. One unusual parameter was robust: the fold-change in β-catenin level (post-Wnt/pre-Wnt). In Xenopus, dorsal-anterior development and target gene expression are robust to perturbations that alter the final level but leave the fold-change intact. These suggest, first, that despite cellular noise, the cell responds reliably to Wnt stimulation by maintaining a robust fold-change in β-catenin. Second, the transcriptional machinery downstream of the Wnt pathway does not simply read the β-catenin level after Wnt stimulation but computes fold-changes in β-catenin. Analogous to Weber's Law in sensory physiology, some gene transcription networks must respond to fold-changes in signals, rather! than absolute levels, which may buffer stochastic, genetic, and environmental variation.
• The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation
  - Mol Cell 36(5):894-899 (2009)
  Many sensory systems (e.g., vision and hearing) show a response that is proportional to the fold-change in the stimulus relative to the background, a feature related to Weber's Law. Recent experiments suggest such a fold-change detection feature in signaling systems in cells: a response that depends on the fold-change in the input signal, and not on its absolute level. It is therefore of interest to find molecular mechanisms of gene regulation that can provide such fold-change detection. Here, we demonstrate theoretically that fold-change detection can be generated by one of the most common network motifs in transcription networks, the incoherent feedforward loop (I1-FFL), in which an activator regulates both a gene and a repressor of the gene. The fold-change detection feature of the I1-FFL applies to the entire shape of the response, including its amplitude and duration, and is valid for a wide range of biochemical parameters.