Latest Articles Include:
- A NEAT Way of Regulating Nuclear Export of mRNAs
Scadden D - Mol Cell 35(4):395-396 (2009)
In this issue of Molecular Cell, Chen and Carmichael (2009) demonstrate that the noncoding RNA NEAT1 regulates gene expression by restricting nuclear export. - Kinky Binding and SECsy Insertions
Morley SJ Willett M - Mol Cell 35(4):396-398 (2009)
Here Budiman et al. (2009) demonstrate that the selective translation of selenocysteine-containing proteins can be regulated by the mutually exclusive binding of eIF4a3 and SECIS binding protein 2 (SBP2) to a cis-acting element in the 3′ untranslated region (3′UTR) of the target mRNA. - Unraveling the Secrets of Regulating Mitochondrial DNA Replication
Klingbeil MM Shapiro TA - Mol Cell 35(4):398-400 (2009)
In this issue, Liu et al. (2009) report that maxicircle DNA copy number in trypanosomes is regulated by proteolysis of a helicase; the complex kinetoplast DNA system yields a clear view of how mitochondrial DNA replication can be regulated. - Ribosome Shifting or Splitting: It Is All Up To the EF-G
Christian B Haque E Spremulli L - Mol Cell 35(4):400-402 (2009)
Mitochondria possess two elongation factor Gs: one with translocation activity (EF-G1mt) and the other with no confirmed activity (EF-G2mt). Tsuboi et al. (2009) now show that the function of EF-G2mt is not in elongation but, rather, in ribosome recycling. - TERRA RNA Binding to TRF2 Facilitates Heterochromatin Formation and ORC Recruitment at Telomeres
Deng Z Norseen J Wiedmer A Riethman H Lieberman PM - Mol Cell 35(4):403-413 (2009)
Telomere-repeat-encoding RNA (referred to as TERRA) has been identified as a potential component of yeast and mammalian telomeres. We show here that TERRA RNA interacts with several telomere-associated proteins, including telomere repeat factors 1 (TRF1) and 2 (TRF2), subunits of the origin recognition complex (ORC), heterochromatin protein 1 (HP1), histone H3 trimethyl K9 (H3 K9me3), and members of the DNA-damage-sensing pathway. siRNA depletion of TERRA caused an increase in telomere dysfunction-induced foci, aberrations in metaphase telomeres, and a loss of histone H3 K9me3 and ORC at telomere repeat DNA. Previous studies found that TRF2 amino-terminal GAR domain recruited ORC to telomeres. We now show that TERRA RNA can interact directly with the TRF2 GAR and ORC1 to form a stable ternary complex. We conclude that TERRA facilitates TRF2 interaction with ORC and plays a central role in telomere structural maintenance and heterochromatin formation. - Loss of Human Ribosomal Gene CpG Methylation Enhances Cryptic RNA Polymerase II Transcription and Disrupts Ribosomal RNA Processing
Gagnon-Kugler T Langlois F Stefanovsky V Lessard F Moss T - Mol Cell 35(4):414-425 (2009)
Epigenetic methyl-CpG silencing of the ribosomal RNA (rRNA) genes is thought to downregulate rRNA synthesis in mammals. In contrast, we now show that CpG methylation in fact positively influences rRNA synthesis and processing. Human HCT116 cells, inactivated for DNMT1 and DNMT3b or treated with aza-dC, lack CpG methylation and reactivate a large fraction of normally silent rRNA genes. Unexpectedly, these cells display reduced rRNA synthesis and processing and accumulate unprocessed 45S rRNA. Reactivation of the rRNA genes is associated with their cryptic transcription by RNA polymerase II. Ectopic expression of cryptic rRNA gene transcripts recapitulates the defects associated with loss of CpG methylation. The data demonstrate that rRNA gene silencing prevents cryptic RNA polymerase II transcription of these genes. Lack of silencing leads to the partial disruption of rRNA synthesis and rRNA processing, providing an explanation for the cytotoxic effects of loss of CpG m! ethylation. - Structure and Function of the PP2A-Shugoshin Interaction
Xu Z Cetin B Anger M Cho US Helmhart W Nasmyth K Xu W - Mol Cell 35(4):426-441 (2009)
Accurate chromosome segregation during mitosis and meiosis depends on shugoshin proteins that prevent precocious dissociation of cohesin from centromeres. Shugoshins associate with PP2A, which is thought to dephosphorylate cohesin and thereby prevent cleavage by separase during meiosis I. A crystal structure of a complex between a fragment of human Sgo1 and an AB′C PP2A holoenzyme reveals that Sgo1 forms a homodimeric parallel coiled coil that docks simultaneously onto PP2A's C and B′ subunits. Sgo1 homodimerization is a prerequisite for PP2A binding. While hSgo1 interacts only with the AB′C holoenzymes, its relative, Sgo2, interacts with all PP2A forms and may thus lead to dephosphorylation of distinct substrates. Mutant shugoshin proteins defective in the binding of PP2A cannot protect centromeric cohesin from separase during meiosis I or support the spindle assembly checkpoint in yeast. Finally, we provide evidence that PP2A's recruitment to chromosomes may be! sufficient to protect cohesin from separase in mammalian oocytes. - The F Box Protein Fbx6 Regulates Chk1 Stability and Cellular Sensitivity to Replication Stress
Zhang YW Brognard J Coughlin C You Z Dolled-Filhart M Aslanian A Manning G Abraham RT Hunter T - Mol Cell 35(4):442-453 (2009)
ATR and Chk1 are two key protein kinases in the replication checkpoint. Activation of ATR-Chk1 has been extensively investigated, but checkpoint termination and replication fork restart are less well understood. Here, we report that DNA damage not only activates Chk1, but also exposes a degron-like region at the carboxyl terminus of Chk1 to an Fbx6-containing SCF (Skp1-Cul1-F box) E3 ligase, which mediates the ubiquitination and degradation of Chk1 and, in turn, terminates the checkpoint. The protein levels of Chk1 and Fbx6 showed an inverse correlation in both cultured cancer cells and in human breast tumor tissues. Further, we show that low levels of Fbx6 and consequent impairment of replication stress-induced Chk1 degradation are associated with cancer cell resistance to the chemotherapeutic agent, camptothecin. We propose that Fbx6-dependent Chk1 degradation contributes to S phase checkpoint termination and that a defect in this mechanism might increase tumor cell ! resistance to certain anticancer drugs. - Common Design Principles in the Spliceosomal RNA Helicase Brr2 and in the Hel308 DNA Helicase
Pena V Jovin SM Fabrizio P Orlowski J Bujnicki JM Lührmann R Wahl MC - Mol Cell 35(4):454-466 (2009)
Brr2 is a unique DExD/H box protein required for catalytic activation and disassembly of the spliceosome. It contains two tandem helicase cassettes that both comprise dual RecA-like domains and a noncanonical Sec63 unit. The latter may bestow the enzyme with unique properties. We have determined crystal structures of the C-terminal Sec63 unit of yeast Brr2, revealing three domains, two of which resemble functional modules of a DNA helicase, Hel308, despite lacking significant sequence similarity. This structural similarity together with sequence conservation between the enzymes throughout the RecA-like domains and a winged helix domain allowed us to devise a structural model of the N-terminal active cassette of Brr2. We consolidated the model by rational mutagenesis combined with splicing and U4/U6 di-snRNA unwinding assays, highlighting how the RecA-like domains and the Sec63 unit form a functional entity that appears suitable for unidirectional and processive RNA dup! lex unwinding during spliceosome activation and disassembly. - Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA
Chen LL Carmichael GG - Mol Cell 35(4):467-478 (2009)
In many cells, mRNAs containing inverted repeats (Alu repeats in humans) in their 3′ untranslated regions (3′UTRs) are inefficiently exported to the cytoplasm. Nuclear retention correlates with adenosine-to-inosine editing and is in paraspeckle-associated complexes containing the proteins p54nrb, PSF, and PSP1α. We report that robust editing activity in human embryonic stem cells (hESCs) does not lead to nuclear retention. p54nrb, PSF, and PSP1α are all expressed in hESCs, but paraspeckles are absent and only appear upon differentiation. Paraspeckle assembly and function depend on expression of a long nuclear-retained noncoding RNA, NEAT1. This RNA is not detectable in hESCs but is induced upon differentiation. Knockdown of NEAT1 in HeLa cells results both in loss of paraspeckles and in enhanced nucleocytoplasmic export of mRNAs containing inverted Alu repeats. Taken together, these results assign a biological function to a large noncoding nuclear RNA in the regu! lation of mRNA export. - Eukaryotic Initiation Factor 4a3 Is a Selenium-Regulated RNA-Binding Protein that Selectively Inhibits Selenocysteine Incorporation
Budiman ME Bubenik JL Miniard AC Middleton LM Gerber CA Cash A Driscoll DM - Mol Cell 35(4):479-489 (2009)
The synthesis of selenoproteins requires the translational recoding of the UGA stop codon as selenocysteine. During selenium deficiency, there is a hierarchy of selenoprotein expression, with certain selenoproteins synthesized at the expense of others. The mechanism by which the limiting selenocysteine incorporation machinery is preferentially utilized to maintain the expression of essential selenoproteins has not been elucidated. Here we demonstrate that eukaryotic initiation factor 4a3 (eIF4a3) is involved in the translational control of a subset of selenoproteins. The interaction of eIF4a3 with the selenoprotein mRNA prevents the binding of SECIS binding protein 2, which is required for selenocysteine insertion, thereby inhibiting the synthesis of the selenoprotein. Furthermore, the expression of eIF4a3 is regulated in response to selenium. Based on knockdown and overexpression studies, eIF4a3 is necessary and sufficient to mediate selective translational repression! in cells. Our results support a model in which eIF4a3 links selenium status with differential selenoprotein expression. - Trypanosomes Have Six Mitochondrial DNA Helicases with One Controlling Kinetoplast Maxicircle Replication
Liu B Wang J Yaffe N Lindsay ME Zhao Z Zick A Shlomai J Englund PT - Mol Cell 35(4):490-501 (2009)
Kinetoplast DNA (kDNA), the trypanosome mitochondrial DNA, contains thousands of minicircles and dozens of maxicircles interlocked in a giant network. Remarkably, Trypanosoma brucei's genome encodes 8 PIF1-like helicases, 6 of which are mitochondrial. We now show that TbPIF2 is essential for maxicircle replication. Maxicircle abundance is controlled by TbPIF2 level, as RNAi of this helicase caused maxicircle loss, and its overexpression caused a 3- to 6-fold increase in maxicircle abundance. This regulation of maxicircle level is mediated by the TbHslVU protease. Previous experiments demonstrated that RNAi knockdown of TbHslVU dramatically increased abundance of minicircles and maxicircles, presumably because a positive regulator of their synthesis escaped proteolysis and allowed synthesis to continue. Here, we found that TbPIF2 level increases following RNAi of the protease. Therefore, this helicase is a TbHslVU substrate and an example of a positive regulator, thus p! roviding a molecular mechanism for controlling maxicircle replication. - EF-G2mt Is an Exclusive Recycling Factor in Mammalian Mitochondrial Protein Synthesis
Tsuboi M Morita H Nozaki Y Akama K Ueda T Ito K Nierhaus KH Takeuchi N - Mol Cell 35(4):502-510 (2009)
Bacterial translation elongation factor G (EF-G) catalyzes translocation during peptide elongation and mediates ribosomal disassembly during ribosome recycling in concert with the ribosomal recycling factor (RRF). Two homologs of EF-G have been identified in mitochondria from yeast to man, EF-G1mt and EF-G2mt. Here, we demonstrate that the dual function of bacterial EF-G is divided between EF-G1mt and EF-G2mt in human mitochondria (RRFmt). EF-G1mt specifically catalyzes translocation, whereas EF-G2mt mediates ribosome recycling with human mitochondrial RRF but lacks translocation activity. Domain swapping experiments suggest that the functional specificity for EF-G2mt resides in domains III and IV. Furthermore, GTP hydrolysis by EF-G2mt is not necessary for ribosomal splitting, in contrast to the bacterial-recycling mode. Because EF-G2mt represents a class of translational GTPase that is involved in ribosome recycling, we propose to rename this factor mitochondrial rib! osome recycling factor 2 (RRF2mt). - RSK Is a Principal Effector of the RAS-ERK Pathway for Eliciting a Coordinate Promotile/Invasive Gene Program and Phenotype in Epithelial Cells
Doehn U Hauge C Frank SR Jensen CJ Duda K Nielsen JV Cohen MS Johansen JV Winther BR Lund LR Winther O Taunton J Hansen SH Frödin M - Mol Cell 35(4):511-522 (2009)
The RAS-stimulated RAF-MEK-ERK pathway confers epithelial cells with critical motile and invasive capacities during development, tissue regeneration, and carcinoma progression, often via promoting the epithelial-mesenchymal transition (EMT). Many mechanisms by which ERK exerts this control remain elusive. We demonstrate that the ERK-activated kinase RSK is necessary to induce mesenchymal motility and invasive capacities in nontransformed epithelial and carcinoma cells. RSK is sufficient to induce certain motile responses. Expression profiling analysis revealed that a primary role of RSK is to induce transcription of a potent promotile/invasive gene program by FRA1-dependent and -independent mechanisms. The program enables RSK to coordinately modulate the extracellular environment, the intracellular motility apparatus, and receptors mediating communication between these compartments to stimulate motility and invasion. These findings uncover a mechanism whereby the RAS-E! RK pathway controls epithelial cell motility by identifying RSK as a key effector, from which emanate multiple highly coordinate transcription-dependent mechanisms for stimulation of motility and invasive properties. - Insights into the Bacterial Transferrin Receptor: The Structure of Transferrin-Binding Protein B from Actinobacillus pleuropneumoniae
Moraes TF Yu RH Strynadka NC Schryvers AB - Mol Cell 35(4):523-533 (2009)
Pathogenic bacteria from the Neisseriaceae and Pasteurellacea families acquire iron directly from the host iron-binding glycoprotein, transferrin (Tf), in a process mediated by surface receptor proteins that directly bind host Tf, extract the iron, and transport it across the outer membrane. The bacterial Tf receptor is comprised of a surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), both of which are essential for survival in the host. In this study, we report the 1.98 Å resolution structure of TbpB from the porcine pathogen Actinobacillus pleuropneumoniae, providing insights into the mechanism of Tf binding and the role of TbpB. A model for the complex of TbpB bound to Tf is proposed. Mutation of a single surface-exposed Phe residue on TbpB within the predicted interface completely abolishes binding to Tf, suggesting that the TbpB N lobe comprises the sole high-affinity binding region for T! f. - A Selective Requirement for 53BP1 in the Biological Response to Genomic Instability Induced by Brca1 Deficiency
Cao L Xu X Bunting SF Liu J Wang RH Cao LL Wu JJ Peng TN Chen J Nussenzweig A Deng CX Finkel T - Mol Cell 35(4):534-541 (2009)
The molecular pathways leading from genomic instability to cellular senescence and/or cell death remain incompletely characterized. Using mouse embryonic fibroblasts with constitutively increased DNA damage due to the absence of the full-length form of the tumor suppressor Brca1 (Brca1Δ11/Δ11), we show that deletion of p53 binding protein 1 (53BP1) selectivity abrogates senescence and cell death stimulated by reduced Brca1 activity. Furthermore, the embryonic lethality induced by Brca1 mutation can be alleviated by 53BP1 deletion. Adult Brca1Δ11/Δ1153BP1−/− manifest constitutively high levels of genomic instability, yet age relatively normally, with a surprisingly low incidence of overall tumor formation. Together, these in vitro and in vivo data suggest that 53BP1 is specifically required for the development of premature senescence and apoptosis induced by Brca1 deficiency. These observations may have important implications for Brca1-mediated tumor formation a! s well as for the molecular pathway leading from genomic instability to organismal aging.
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