Hot off the presses! Mar 18 mol cell

The Mar 18 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:

• Moving in for the Kill: Activation of an Endoribonuclease Toxin by a Quorum-Sensing Peptide
  - mol cell 41(6):617-618 (2011)
  Extracellular death factor is a quorum-sensing pentapeptide that relays cell density information to an intracellular toxin-antitoxin complex. In this issue of Molecular Cell, Belitsky et al. (2011) demonstrate that the peptide competes with the antitoxin for toxin binding and directly activates the latter's endoribonuclease activity.
• Regulatory Posttranslational Modifications in Hsp90 Can Be Compensated by Cochaperone Aha1
  - mol cell 41(6):619-620 (2011)
  In this issue of Molecular Cell, Mollapour et al. (2011) show that phosphorylation of Hsp90 affects the ATPase function, chaperone function, and cochaperone binding in various ways. Several impacts can be compensated by overexpression of the cochaperone Aha1.
• UPF1 Learns to Relax and Unwind
  - mol cell 41(6):621-623 (2011)
  In this issue of Molecular Cell, Chakrabarti et al. (2011) structurally reveal how UPF1, an RNA helicase that plays a central role in nonsense-mediated mRNA decay, is conformationally converted from a largely inactive state to an active state upon UPF2 binding.
• The Escherichia coli Extracellular Death Factor EDF Induces the Endoribonucleolytic Activities of the Toxins MazF and ChpBK
  - mol cell 41(6):625-635 (2011)
  Escherichia coli (E. coli) mazEF is a toxin-antitoxin (TA) stress-induced module that mediates cell death requiring the quorum-sensing pentapeptide NNWNN designated EDF (extracellular death factor). E. coli toxin MazF is a sequence-specific endoribonuclease cleaving single-stranded mRNAs at ACA sequences. E. coli ChpBK, a toxin homologous to MazF, is a sequence-specific endoribonuclease cleaving single-stranded mRNAs at ACA, ACG, and ACU sequences. Here we report that, in vitro, the signaling molecule EDF significantly amplifies the endoribonucleolytic activities of both MazF and ChpBK. EDF also overcomes the inhibitory activity of the antitoxins MazE over the toxin MazF and ChpBI over ChpBK. EDF sequence is important for both functions. Moreover, direct sequence-specific binding of EDF to MazF has been confirmed. Peptide-protein modeling revealed parallel contacts between EDF-MazF and MazE-MazF. These findings are intriguing, since most known quorum-sensing molecules ! monitor gene expression on the transcriptional level, while EDF monitors posttranscriptionally.
• Inhibition of Protein Phosphatase 2A Activity by PI3Kγ Regulates β-Adrenergic Receptor Function
  - mol cell 41(6):636-648 (2011)
  Phosphoinositide 3-kinase γ (PI3Kγ) is activated by G protein-coupled receptors (GPCRs). We show here that PI3Kγ inhibits protein phosphatase 2A (PP2A) at the β-adrenergic receptor (βAR, a GPCR) complex altering G protein coupling. PI3Kγ inhibition results in significant increase of βAR-associated phosphatase activity leading to receptor dephosphorylation and resensitization preserving cardiac function. Mechanistically, PI3Kγ inhibits PP2A activity at the βAR complex by phosphorylating an intracellular inhibitor of PP2A (I2PP2A) on serine residues 9 and 93, resulting in enhanced binding to PP2A. Indeed, enhanced phosphorylation of β2ARs is observed with a phosphomimetic I2PP2A mutant that was completely reversed with a mutant mimicking dephosphorylated state. siRNA depletion of endogenous I2PP2A augments PP2A activity despite active PI3K resulting in β2AR dephosphorylation and sustained signaling. Our study provides the underpinnings of a PI3Kγ-mediated reg! ulation of PP2A activity that has significant consequences on receptor function with broad implications in cellular signaling.
• Calmodulin-Dependent Activation of MAP Kinase for ROS Homeostasis in Arabidopsis
  - mol cell 41(6):649-660 (2011)
  Rapid recognition and signal transduction of mechanical wounding through various signaling molecules, including calcium (Ca2+), protein phosphorylation, and reactive oxygen species (ROS), are necessary early events leading to stress resistance in plants. Here we report that an Arabidopsis mitogen-activated protein kinase 8 (MPK8) connects protein phosphorylation, Ca2+, and ROS in the wound-signaling pathway. MPK8 is activated through mechanical wounding, and this activation requires direct binding of calmodulins (CaMs) in a Ca2+-dependent manner. MPK8 is also phosphorylated and activated by a MAPKK MKK3 in the prototypic kinase cascade, and full activation of MPK8 needs both CaMs and MKK3 in planta. The MPK8 pathway negatively regulates ROS accumulation through controlling expression of the Rboh D gene. These findings suggest that two major activation modes in eukaryotes, Ca2+/CaMs and the MAP kinase phosphorylation cascade, converge at MPK8 to monitor or maintain an e! ssential part of ROS homeostasis.
• ERK-MAPK Drives Lamellipodia Protrusion by Activating the WAVE2 Regulatory Complex
  - mol cell 41(6):661-671 (2011)
  Cell movement begins with a leading edge protrusion, which is stabilized by nascent adhesions and retracted by mature adhesions. The ERK-MAPK (extracellular signal-regulated kinase-mitogen-activated protein kinase) localizes to protrusions and adhesions, but how it regulates motility is not understood. We demonstrate that ERK controls protrusion initiation and protrusion speed. Lamellipodial protrusions are generated via the WRC (WAVE2 regulatory complex), which activates the Arp2/3 actin nucleator for actin assembly. The WRC must be phosphorylated to be activated, but the sites and kinases that regulate its intermolecular changes and membrane recruitment are unknown. We show that ERK colocalizes with the WRC at lamellipodial leading edges and directly phosphorylates two WRC components: WAVE2 and Abi1. The phosphorylations are required for functional WRC interaction with Arp2/3 and actin during cell protrusion. Thus, ERK coordinates adhesion disassembly with WRC activa! tion and actin polymerization to promote productive leading edge advancement during cell migration.
• Threonine 22 Phosphorylation Attenuates Hsp90 Interaction with Cochaperones and Affects Its Chaperone Activity
  - mol cell 41(6):672-681 (2011)
  Heat shock protein 90 (Hsp90) is an essential molecular chaperone whose activity is regulated not only by cochaperones but also by distinct posttranslational modifications. We report here that casein kinase 2 phosphorylates a conserved threonine residue (T22) in α helix-1 of the yeast Hsp90 N-domain both in vitro and in vivo. This α helix participates in a hydrophobic interaction with the catalytic loop in Hsp90's middle domain, helping to stabilize the chaperone's ATPase-competent state. Phosphomimetic mutation of this residue alters Hsp90 ATPase activity and chaperone function and impacts interaction with the cochaperones Aha1 and Cdc37. Overexpression of Aha1 stimulates the ATPase activity, restores cochaperone interactions, and compensates for the functional defects of these Hsp90 mutants.
• Ligand-Driven Vectorial Folding of Ribosome-Bound Human CFTR NBD1
  - mol cell 41(6):682-692 (2011)
  The mechanism by which protein folding is coupled to biosynthesis is a critical, but poorly understood, aspect of protein conformational diseases. Here we use fluorescence resonance energy transfer (FRET) to characterize tertiary structural transitions of nascent polypeptides and show that the first nucleotide-binding domain (NBD1) of human CFTR, whose folding is defective in cystic fibrosis, folds via a cotranslational multistep pathway as it is synthesized on the ribosome. Folding begins abruptly as NBD1 residues 389–500 emerge from the ribosome exit tunnel, initiating compaction of a small, N-terminal α/β-subdomain. Real-time kinetics of synchronized nascent chains revealed that subdomain folding is rapid, occurs coincident with synthesis, and is facilitated by direct ATP binding to the nascent polypeptide. These findings localize the major CF defect late in the NBD1 folding pathway and establish a paradigm wherein a cellular ligand promotes vectorial domain fol! ding by facilitating an energetically favored local peptide conformation.
• Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and Its Regulation by Upf2
  - mol cell 41(6):693-703 (2011)
  Upf1 is a crucial factor in nonsense-mediated mRNA decay, the eukaryotic surveillance pathway that degrades mRNAs containing premature stop codons. The essential RNA-dependent ATPase activity of Upf1 is triggered by the formation of the surveillance complex with Upf2-Upf3. We report crystal structures of Upf1 in the presence and absence of the CH domain, captured in the transition state with ADP:AlF4− and RNA. In isolation, Upf1 clamps onto the RNA, enclosing it in a channel formed by both the catalytic and regulatory domains. Upon binding to Upf2, the regulatory CH domain of Upf1 undergoes a large conformational change, causing the catalytic helicase domain to bind RNA less extensively and triggering its helicase activity. Formation of the surveillance complex thus modifies the RNA binding properties and the catalytic activity of Upf1, causing it to switch from an RNA-clamping mode to an RNA-unwinding mode.
• Chromatin-Associated Protein Kinase C-θ Regulates an Inducible Gene Expression Program and MicroRNAs in Human T Lymphocytes
  - mol cell 41(6):704-719 (2011)
  Studies in yeast demonstrate that signaling kinases have a surprisingly active role in the nucleus, where they tether to chromatin and modulate gene expression programs. Despite these seminal studies, the nuclear mechanism of how signaling kinases control transcription of mammalian genes is in its infancy. Here, we provide evidence for a hitherto unknown function of protein kinase C-theta (PKC-θ), which physically associates with the regulatory regions of inducible immune response genes in human T cells. Chromatin-anchored PKC-θ forms an active nuclear complex by interacting with RNA polymerase II, the histone kinase MSK-1, and the adaptor molecule 14-3-3ζ. ChIP-on-chip reveals that PKC-θ binds to promoters and transcribed regions of genes, as well as to microRNA promoters that are crucial for cytokine regulation. Our results provide a molecular explanation for the role of PKC-θ not only in normal T cell function, but also in circumstances of its ectopic expressio! n in cancer.
• The Replicase Sliding Clamp Dynamically Accumulates behind Progressing Replication Forks in Bacillus subtilis Cells
  - mol cell 41(6):720-732 (2011)
  The sliding clamp is an essential component of the replisome required for processivity of DNA synthesis and several other aspects of chromosome metabolism. However, the in vivo dynamics of the clamp are poorly understood. We have used various biochemical and cell biological methods to study the dynamics of clamp association with the replisome in Bacillus subtilis cells. We find that clamps form large assemblies on DNA, called "clamp zones." Loading depends on DnaG primase and is probably driven by Okazaki fragment initiation on the lagging strand. Unloading, which is probably regulated, only occurs after many clamps have accumulated on the DNA. On/off cycling allows chromosomal zones of about 200 accumulated clamps to follow the replisome. Since we also show that clamp zones recruit proteins bearing a clamp-binding sequence to replication foci, the results highlight the clamp as a central organizer in the structure and function of replication foci.
• Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay
  - mol cell 41(6):733-746 (2011)
  Short hairpin RNAs (shRNAs) provide powerful experimental tools by enabling stable and regulated gene silencing through programming of endogenous microRNA pathways. Since requirements for efficient shRNA biogenesis and target suppression are largely unknown, many predicted shRNAs fail to efficiently suppress their target. To overcome this barrier, we developed a "Sensor assay" that enables the biological identification of effective shRNAs at large scale. By constructing and evaluating 20,000 RNAi reporters covering every possible target site in nine mammalian transcripts, we show that our assay reliably identifies potent shRNAs that are surprisingly rare and predominantly missed by existing algorithms. Our unbiased analyses reveal that potent shRNAs share various predicted and previously unknown features associated with specific microRNA processing steps, and suggest a model for competitive strand selection. Together, our study establishes a powerful tool for large! -scale identification of highly potent shRNAs and provides insights into sequence requirements of effective RNAi.