Hot off the presses! Aug 19 Mol Cell

The Aug 19 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:

• Simple Rules for Complex Processes: New Lessons from the Budding Yeast Cell Cycle
  - Mol Cell 43(4):497-500 (2011)
  Two papers in this issue of Molecular Cell, Doncic et al. (2011) and Eser et al. (2011), present some satisfyingly simple ideas for the organization of the complex network that controls cell cycle progression and cell fate specification in budding yeast.
• Functional Expansion of the tRNA World under Stress
  - Mol Cell 43(4):500-502 (2011)
  In this issue of Molecular Cell, Ivanov et al. (2011) provide mechanistic insight into tRNA fragment-based translational regulation to expand our understanding of the nondecoding roles of tRNA.
• Regional Specialization: The NEXT Big Thing in Nuclear RNA Turnover
  - Mol Cell 43(4):502-504 (2011)
  Distinct heteromeric protein adaptors feed RNA substrates to the ribonucleolytic exosome in different regions of the human nucleus; the nuclear exosome targeting (NEXT) complex, described in this issue of Molecular Cell by Lubas et al. (2011), operates in nonnucleolar regions.
• Integrated Gene Regulatory Circuits: Celebrating the 50th Anniversary of the Operon Model
  - Mol Cell 43(4):505-514 (2011)
  In 1961, François Jacob and Jacques Monod presented a landmark paper describing the operon model. The meeting held in Institut Pasteur this May to celebrate the 50th anniversary of their seminal discovery highlighted the impact their visionary theory has had on our understanding of gene regulation. The concepts they postulated are indeed at the heart of two major mechanisms that underlie the control of gene expression in both prokaryotes and eukaryotes: the regulation of transcription initiation by specific DNA-binding proteins, and posttranscriptional control by noncoding RNAs. The model also promoted the concept of regulatory circuits in biology in general and was a precursor for present-day systems biology.
• Commitment to a Cellular Transition Precedes Genome-wide Transcriptional Change
  - Mol Cell 43(4):515-527 (2011)
  In budding yeast, commitment to cell division corresponds to activating the positive feedback loop of G1 cyclins controlled by the transcription factors SBF and MBF. This pair of transcription factors has over 200 targets, implying that cell-cycle commitment coincides with genome-wide changes in transcription. Here, we find that genes within this regulon have a well-defined distribution of transcriptional activation times. Combinatorial use of SBF and MBF results in a logical OR function for gene expression and partially explains activation timing. Activation of G1 cyclin expression precedes the activation of the bulk of the G1/S regulon, ensuring that commitment to cell division occurs before large-scale changes in transcription. Furthermore, we find similar positive feedback-first regulation in the yeasts S. bayanus and S. cerevisiae, as well as human cells. The widespread use of the feedback-first motif in eukaryotic cell-cycle control, implemented by nonorthologous! proteins, suggests its frequent deployment at cellular transitions.
• Distinct Interactions Select and Maintain a Specific Cell Fate
  - Mol Cell 43(4):528-539 (2011)
  The ability to specify and maintain discrete cell fates is essential for development. However, the dynamics underlying selection and stability of distinct cell types remain poorly understood. Here, we provide a quantitative single-cell analysis of commitment dynamics during the mating-mitosis switch in budding yeast. Commitment to division corresponds precisely to activating the G1 cyclin positive feedback loop in competition with the cyclin inhibitor Far1. Cyclin-dependent phosphorylation and inhibition of the mating pathway scaffold Ste5 are required to ensure exclusive expression of the mitotic transcriptional program after cell cycle commitment. Failure to commit exclusively results in coexpression of both cell cycle and pheromone-induced genes, and a morphologically mixed inviable cell fate. Thus, specification and maintenance of a cellular state are performed by distinct interactions, which are likely a consequence of disparate reaction rates and may be a general! feature of the interlinked regulatory networks responsible for selecting cell fates.
• Robust Spindle Alignment in Drosophila Neuroblasts by Ultrasensitive Activation of Pins
  - Mol Cell 43(4):540-549 (2011)
  Cellular signaling pathways exhibit complex response profiles with features such as thresholds and steep activation (i.e., ultrasensitivity). In a reconstituted mitotic spindle orientation pathway, activation of Drosophila Pins (LGN in mammals) by Gαi is ultrasensitive (apparent Hill coefficient of 3.1), such that Pins recruitment of the microtubule binding protein Mud (NuMA) occurs over a very narrow Gαi concentration range. Ultrasensitivity is required for Pins function in neuroblasts as a nonultrasensitive Pins mutant fails to robustly couple spindle position to cell polarity. Pins contains three Gαi binding GoLoco domains (GLs); Gαi binding to GL3 activates Pins, whereas GLs 1 and 2 shape the response profile. Although cooperative binding is one mechanism for generating ultrasensitivity, we find GLs 1 and 2 act as "decoys" that compete against activation at GL3. Many signaling proteins contain multiple protein interaction domains, and the decoy mechanism ma! y be a common method for generating ultrasensitivity in regulatory pathways.
• Regulatory Cohesion of Cell Cycle and Cell Differentiation through Interlinked Phosphorylation and Second Messenger Networks
  - Mol Cell 43(4):550-560 (2011)
  In Caulobacter crescentus, phosphorylation of key regulators is coordinated with the second messenger cyclic di-GMP to drive cell-cycle progression and differentiation. The diguanylate cyclase PleD directs pole morphogenesis, while the c-di-GMP effector PopA initiates degradation of the replication inhibitor CtrA by the AAA+ protease ClpXP to license S phase entry. Here, we establish a direct link between PleD and PopA reliant on the phosphodiesterase PdeA and the diguanylate cyclase DgcB. PdeA antagonizes DgcB activity until the G1-S transition, when PdeA is degraded by the ClpXP protease. The unopposed DgcB activity, together with PleD activation, upshifts c-di-GMP to drive PopA-dependent CtrA degradation and S phase entry. PdeA degradation requires CpdR, a response regulator that delivers PdeA to the ClpXP protease in a phosphorylation-dependent manner. Thus, CpdR serves as a crucial link between phosphorylation pathways and c-di-GMP metabolism to mediate protein de! gradation events that irreversibly and coordinately drive bacterial cell-cycle progression and development.
• The CDG1 Kinase Mediates Brassinosteroid Signal Transduction from BRI1 Receptor Kinase to BSU1 Phosphatase and GSK3-like Kinase BIN2
  - Mol Cell 43(4):561-571 (2011)
  The brassinosteroid (BR) signaling pathway includes two receptor-like kinases (BRI1 and BAK1), a plasma membrane-associated kinase (BSK1), two phosphatases (BSU1 and PP2A), a GSK3-like kinase (BIN2), and two homologous transcription factors (BZR1 and BES1/BZR2). But the mechanisms of signal relay are not fully understood. Here, we show that a receptor-like cytoplasmic kinase named CDG1 mediates signal transduction from BRI1 to BSU1. Transgenic experiments confirm that CDG1 and its homolog CDL1 positively regulate BR signaling and plant growth. Mass spectrometry analysis identified BRI1 phosphorylation sites in CDG1 and CDG1 phosphorylation sites in BSU1. Mutations of these phosphorylation sites compromised the BR signaling functions. The results demonstrate that BRI1 phosphorylates S234 to activate CDG1 kinase, and CDG1 in turn phosphorylates S764 to activate BSU1, which inactivates BIN2 by dephosphorylating Y200 of BIN2. This study thus demonstrates a complete phospho! rylation/dephosphorylation cascade linking a steroid-activated receptor kinase to a GSK3-like kinase in plants.
• Hsp90-Cdc37 Chaperone Complex Regulates Ulk1- and Atg13-Mediated Mitophagy
  - Mol Cell 43(4):572-585 (2011)
  Autophagy, the primary recycling pathway of cells, plays a critical role in mitochondrial quality control under normal growth conditions and in the response to cellular stress. The Hsp90-Cdc37 chaperone complex coordinately regulates the activity of select kinases to orchestrate many facets of the stress response. Although both maintain mitochondrial integrity, the relationship between Hsp90-Cdc37 and autophagy has not been well characterized. Ulk1, one of the mammalian homologs of yeast Atg1, is a serine-threonine kinase required for mitophagy. Here we show that the interaction between Ulk1 and Hsp90-Cdc37 stabilizes and activates Ulk1, which in turn is required for the phosphorylation and release of Atg13 from Ulk1, and for the recruitment of Atg13 to damaged mitochondria. Hsp90-Cdc37, Ulk1, and Atg13 phosphorylation are all required for efficient mitochondrial clearance. These findings establish a direct pathway that integrates Ulk1- and Atg13-directed mitophagy wit! h the stress response coordinated by Hsp90 and Cdc37.
• Liprin-Mediated Large Signaling Complex Organization Revealed by the Liprin-α/CASK and Liprin-α/Liprin-β Complex Structures
  - Mol Cell 43(4):586-598 (2011)
  Liprins are highly conserved scaffold proteins that regulate cell adhesion, cell migration, and synapse development by binding to diverse target proteins. The molecular basis governing liprin/target interactions is poorly understood. The liprin-α2/CASK complex structure solved here reveals that the three SAM domains of liprin-α form an integrated supramodule that binds to the CASK kinase-like domain. As supported by biochemical and cellular studies, the interaction between liprin-α and CASK is unique to vertebrates, implying that the liprin-α/CASK interaction is likely to regulate higher-order brain functions in mammals. Consistently, we demonstrate that three recently identified X-linked mental retardation mutants of CASK are defective in binding to liprin-α. We also solved the liprin-α/liprin-β SAM domain complex structure, which uncovers the mechanism underlying liprin heterodimerizaion. Finally, formation of the CASK/liprin-α/liprin-β ternary complex sugge! sts that liprins can mediate assembly of target proteins into large protein complexes capable of regulating numerous cellular activities.
• Ube2w and Ataxin-3 Coordinately Regulate the Ubiquitin Ligase CHIP
  - Mol Cell 43(4):599-612 (2011)
  The mechanisms by which ubiquitin ligases are regulated remain poorly understood. Here we describe a series of molecular events that coordinately regulate CHIP, a neuroprotective E3 implicated in protein quality control. Through their opposing activities, the initiator E2, Ube2w, and the specialized deubiquitinating enzyme (DUB), ataxin-3, participate in initiating, regulating, and terminating the CHIP ubiquitination cycle. Monoubiquitination of CHIP by Ube2w stabilizes the interaction between CHIP and ataxin-3, which through its DUB activity limits the length of chains attached to CHIP substrates. Upon completion of substrate ubiquitination, ataxin-3 deubiquitinates CHIP, effectively terminating the reaction. Our results suggest that functional pairing of E3s with ataxin-3 or similar DUBs represents an important point of regulation in ubiquitin-dependent protein quality control. In addition, the results shed light on disease pathogenesis in SCA3, a neurodegenerative d! isorder caused by polyglutamine expansion in ataxin-3.
• Angiogenin-Induced tRNA Fragments Inhibit Translation Initiation
  - Mol Cell 43(4):613-623 (2011)
  Angiogenin is a stress-activated ribonuclease that cleaves tRNA within anticodon loops to produce tRNA-derived stress-induced fragments (tiRNAs). Transfection of natural or synthetic tiRNAs inhibits protein synthesis and triggers the phospho-eIF2α-independent assembly of stress granules (SGs), essential components of the stress response program. We show that selected tiRNAs inhibit protein synthesis by displacing eIF4G/eIF4A from uncapped > capped RNAs. tiRNAs also displace eIF4F, but not eIF4E:4EBP1, from isolated m7G cap. We identify a terminal oligoguanine motif that is required to displace the eIF4F complex, inhibit translation, and induce SG assembly. We show that the tiRNA-associated translational silencer YB-1 contributes to angiogenin-, tiRNA-, and oxidative stress-induced translational repression. Our data reveal some of the mechanisms by which stress-induced tRNA cleavage inhibits protein synthesis and activates a cytoprotective stress response program.
• Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex
  - Mol Cell 43(4):624-637 (2011)
  The RNA exosome is a conserved degradation machinery, which obtains full activity only when associated with cofactors. The most prominent activator of the yeast nuclear exosome is the RNA helicase Mtr4p, acting in the context of the Trf4p/Air2p/Mtr4p polyadenylation (TRAMP) complex. The existence of a similar activator(s) in humans remains elusive. By establishing an interaction network of the human nuclear exosome, we identify the trimeric Nuclear Exosome Targeting (NEXT) complex, containing hMTR4, the Zn-knuckle protein ZCCHC8, and the putative RNA binding protein RBM7. ZCCHC8 and RBM7 are excluded from nucleoli, and consistently NEXT is specifically required for the exosomal degradation of promoter upstream transcripts (PROMPTs). We also detect putative homolog TRAMP subunits hTRF4-2 (Trf4p) and ZCCHC7 (Air2p) in hRRP6 and hMTR4 precipitates. However, at least ZCCHC7 function is restricted to nucleoli. Our results suggest that human nuclear exosome degradation pathw! ays comprise modules of spatially organized cofactors that diverge from the yeast model.
• Identification of a Rapidly Formed Nonnucleosomal Histone-DNA Intermediate that Is Converted into Chromatin by ACF
  - Mol Cell 43(4):638-648 (2011)
  Chromatin assembly involves the combined action of histone chaperones and ATP-dependent motor proteins. Here, we investigate the mechanism of nucleosome assembly with a purified chromatin assembly system containing the histone chaperone NAP1 and the ATP-dependent motor protein ACF. These studies revealed the rapid formation of a stable nonnucleosomal histone-DNA intermediate that is converted into canonical nucleosomes by ACF. The histone-DNA intermediate does not supercoil DNA like a canonical nucleosome, but has a nucleosome-like appearance by atomic force microscopy. This intermediate contains all four core histones, lacks NAP1, and is formed by the initial deposition of histones H3-H4. Conversion of the intermediate into histone H1-containing chromatin results in increased resistance to micrococcal nuclease digestion. These findings suggest that the histone-DNA intermediate corresponds to nascent nucleosome-like structures, such as those observed at DNA replication! forks. Related complexes might be formed during other chromatin-directed processes such as transcription, DNA repair, and histone exchange.
• The hMsh2-hMsh6 Complex Acts in Concert with Monoubiquitinated PCNA and Pol η in Response to Oxidative DNA Damage in Human Cells
  - Mol Cell 43(4):649-662 (2011)
  Posttranslational modification of PCNA by ubiquitin plays an important role in coordinating the processes of DNA damage tolerance during DNA replication. The monoubiquitination of PCNA was shown to facilitate the switch between the replicative DNA polymerase with the low-fidelity polymerase eta (η) to bypass UV-induced DNA lesions during replication. Here, we show that in response to oxidative stress, PCNA becomes transiently monoubiquitinated in an S phase- and USP1-independent manner. Moreover, Polη interacts with mUb-PCNA at sites of oxidative DNA damage via its PCNA-binding and ubiquitin-binding motifs. Strikingly, while functional base excision repair is not required for this modification of PCNA or Polη recruitment to chromatin, the presence of hMsh2-hMsh6 is indispensable. Our findings highlight an alternative pathway in response to oxidative DNA damage that may coordinate the removal of oxidatively induced clustered DNA lesions and could explain the high lev! els of oxidized DNA lesions in MSH2-deficient cells.
• RB Restricts DNA Damage-Initiated Tumorigenesis through an LXCXE-Dependent Mechanism of Transcriptional Control
  - Mol Cell 43(4):663-672 (2011)
  The LXCXE peptide motif facilitates interaction between the RB tumor suppressor and a large number of cellular proteins that are expected to impinge on diverse biological processes. In vitro and in vivo analyses demonstrated that LXCXE binding function is dispensable for RB promoter association and control of basal gene expression. Dependence on this function of RB is unmasked after DNA damage, wherein LXCXE binding is essential for exerting control over E2F3 and suppressing cell-cycle progression in the presence of genotoxic stress. Gene expression profiling revealed that the transcriptional program coordinated by this specific aspect of RB is associated with progression of human hepatocellular carcinoma and poor disease outcome. Consistent with these findings, biological challenge revealed a requirement for LXCXE binding in suppression of genotoxin-initiated hepatocellular carcinoma in vivo. Together, these studies establish an essential role of the LXCXE binding mot! if for RB-mediated transcriptional control, response to genotoxic insult, and tumor suppression.
• p53-Dependent Transcription and Tumor Suppression Are Not Affected in Set7/9-Deficient Mice
  - Mol Cell 43(4):673-680 (2011)
  Methylation of specific lysine residues in the C terminus of p53 is thought to govern p53-dependent transcription following genotoxic and oncogenic stress. In particular, Set7/9 (KMT7)-mediated monomethylation of human p53 at lysine 372 (p53K372me1) was suggested to be essential for p53 activation in human cell lines. This finding was confirmed in a Set7/9 knockout mouse model (Kurash et al., 2008). In an independent knockout mouse strain deficient in Set7/9, we have investigated its involvement in p53 regulation and find that cells from these mice are normal in their ability to induce p53-dependent transcription following genotoxic and oncogenic insults. Most importantly, we detect no impairment in canonical p53 functions in these mice, indicating that Set7/9-mediated methylation of p53 does not seem to represent a major regulatory event and does not appreciably control p53 activity in vivo.
• The Methyltransferase Set7/9 (Setd7) Is Dispensable for the p53-Mediated DNA Damage Response In Vivo
  - Mol Cell 43(4):681-688 (2011)
  p53 is the central regulator of cell fate following genotoxic stress and oncogene activation. Its activity is controlled by several posttranslational modifications. Originally defined as a critical layer of p53 regulation in human cell lines, p53 lysine methylation by Set7/9 (also called Setd7) was proposed to fulfill a similar function in vivo in the mouse, promoting p53 acetylation, stabilization, and activation upon DNA damage (Kurash et al., 2008). We tested the physiological relevance of this circuit in an independent Set7/9 knockout mouse strain. Deletion of Set7/9 had no effect on p53-dependent cell-cycle arrest or apoptosis following sublethal or lethal DNA damage induced by radiation or genotoxic agents. Set7/9 was also dispensable for p53 acetylation following irradiation. c-myc oncogene-induced apoptosis was also independent of Set7/9, and analysis of p53 target genes showed that Set7/9 is not required for the p53-dependent gene expression program. Our data ! indicate that Set7/9 is dispensable for p53 function in the mouse.
• The Ripoptosome, a Signaling Platform that Assembles in Response to Genotoxic Stress and Loss of IAPs
  - Mol Cell 43(4):689 (2011)