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https://www.readbyqxmd.com/read/28077875/structural-basis-of-co-translational-quality-control-by-arfa-and-rf2-bound-to-ribosome
#1
Fuxing Zeng, Yanbo Chen, Jonathan Remis, Mrinal Shekhar, James C Phillips, Emad Tajkhorshid, Hong Jin
Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28065601/initiation-of-quality-control-during-poly-a-translation-requires-site-specific-ribosome-ubiquitination
#2
Szymon Juszkiewicz, Ramanujan S Hegde
Diverse cellular stressors have been observed to trigger site-specific ubiquitination on several ribosomal proteins. However, the ubiquitin ligases, biochemical consequences, and physiologic pathways linked to these modifications are not known. Here, we show in mammalian cells that the ubiquitin ligase ZNF598 is required for ribosomes to terminally stall during translation of poly(A) sequences. ZNF598-mediated stalling initiated the ribosome-associated quality control (RQC) pathway for degradation of nascent truncated proteins...
December 22, 2016: Molecular Cell
https://www.readbyqxmd.com/read/28008922/atp-hydrolysis-by-upf1-is-required-for-efficient-translation-termination-at-premature-stop-codons
#3
Lucas D Serdar, DaJuan L Whiteside, Kristian E Baker
Nonsense-mediated mRNA decay (NMD) represents a eukaryotic quality control pathway that recognizes and rapidly degrades transcripts harbouring nonsense mutations to limit accumulation of non-functional and potentially toxic truncated polypeptides. A critical component of the NMD machinery is UPF1, an RNA helicase whose ATPase activity is essential for NMD, but for which the precise function and site of action remain unclear. We provide evidence that ATP hydrolysis by UPF1 is required for efficient translation termination and ribosome release at a premature termination codon...
December 23, 2016: Nature Communications
https://www.readbyqxmd.com/read/27995908/structural-insights-into-ribosomal-rescue-by-dom34-and-hbs1-at-near-atomic-resolution
#4
Tarek Hilal, Hiroshi Yamamoto, Justus Loerke, Jörg Bürger, Thorsten Mielke, Christian M T Spahn
The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational machinery. During ribosomal rescue, arrested ribosomes are specifically recognized by the conserved eukaryotic proteins Dom34 and Hbs1, to initiate their recycling. Here we solve the structure of Dom34 and Hbs1 bound to a yeast ribosome programmed with a nonstop mRNA at 3.3 Å resolution using cryo-electron microscopy...
December 20, 2016: Nature Communications
https://www.readbyqxmd.com/read/27986852/structure-of-a-30s-pre-initiation-complex-stalled-by-ge81112-reveals-structural-parallels-in-bacterial-and-eukaryotic-protein-synthesis-initiation-pathways
#5
Jorge P López-Alonso, Attilio Fabbretti, Tatsuya Kaminishi, Idoia Iturrioz, Letizia Brandi, David Gil-Carton, Claudio O Gualerzi, Paola Fucini, Sean R Connell
In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy...
December 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27980192/rescuing-stalled-ribosomes
#6
EDITORIAL
Valda Vinson
No abstract text is available yet for this article.
December 16, 2016: Science
https://www.readbyqxmd.com/read/27934701/translational-termination-without-a-stop-codon
#7
Nathan R James, Alan Brown, Yuliya Gordiyenko, V Ramakrishnan
Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state...
December 16, 2016: Science
https://www.readbyqxmd.com/read/27920294/effects-of-increasing-the-affinity-of-card-for-rna-polymerase-on-mycobacterium-tuberculosis-growth-rrna-transcription-and-virulence
#8
Ashley L Garner, Jayan Rammohan, Jeremy P Huynh, Lucas M Onder, James Chen, Brian Bae, Drake Jensen, Leslie A Weiss, Ana Ruiz Manzano, Seth A Darst, Elizabeth A Campbell, Bryce E Nickels, Eric A Galburt, Christina L Stallings
: CarD is an essential RNA polymerase (RNAP) interacting protein in Mycobacterium tuberculosis (Mtb) that stimulates formation of RNAP-promoter open complexes. CarD plays a complex role in Mtb growth and virulence that is not fully understood. Therefore, to gain further insight into the role of CarD in Mtb growth and virulence we determined the effect of increasing the affinity of CarD for RNAP. Using site-directed mutagenesis guided by crystal structures of CarD bound to RNAP, we identified amino acid substitutions that increase the affinity of CarD for RNAP...
December 5, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27906650/structure-of-the-70s-ribosome-from-human-pathogen-staphylococcus-aureus
#9
Iskander Khusainov, Quentin Vicens, Anthony Bochler, François Grosse, Alexander Myasnikov, Jean-François Ménétret, Johana Chicher, Stefano Marzi, Pascale Romby, Gulnara Yusupova, Marat Yusupov, Yaser Hashem
Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the importance of such features may be less obvious within more closely related organisms, their existence could account for vital yet species-specific mechanisms of translation regulation that would involve stalling, cell survival and antibiotic resistance. Here, we present the first full 70S ribosome structure from Staphylococcus aureus, a Gram-positive pathogenic bacterium, solved by cryo-electron microscopy...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27906161/structural-basis-for-arfa-rf2-mediated-translation-termination-on-mrnas-lacking-stop-codons
#10
Paul Huter, Claudia Müller, Bertrand Beckert, Stefan Arenz, Otto Berninghausen, Roland Beckmann, Daniel N Wilson
In bacteria, ribosomes stalled on truncated mRNAs lacking a stop codon are rescued by either the transfer-messenger RNA (tmRNA), alternative rescue factor A (ArfA) or ArfB rescue systems(1). While tmRNA- and ArfB-ribosome structures have been elucidated(2-7), structural insight into how ArfA recognizes the presence of truncated mRNAs and recruits the canonical termination release factor RF2 to rescue the stalled ribosomes is lacking. Here we present a cryo-electron microscopy reconstruction of a ribosome stalled on a truncated mRNA in the presence of ArfA and RF2...
December 1, 2016: Nature
https://www.readbyqxmd.com/read/27906160/mechanistic-insights-into-the-alternative-translation-termination-by-arfa-and-rf2
#11
Chengying Ma, Daisuke Kurita, Ningning Li, Yan Chen, Hyouta Himeno, Ning Gao
During cellular translation of mRNAs by ribosomes, various situations that would result in the pausing or stalling of translation apparatus at elongation and termination steps often occur(1-6). Except for programmed stalling, which is usually utilized by the cells to exert regulatory purposes(5,7,8), ribosomes stalled on mRNAs need to be terminated and recycled to maintain adequate cellular translation capacity(9). A large source of ribosome stalling originates in aberrant mRNAs that lack a stop codon. Transcriptional errors and misprocessing of primary transcripts, as well as undesired mRNA cleavage, all contribute to the formation of non-stop mRNAs...
December 1, 2016: Nature
https://www.readbyqxmd.com/read/27892503/trans-translation-is-essential-in-the-human-pathogen-legionella-pneumophila
#12
Romain Brunel, Xavier Charpentier
Trans-translation is a ubiquitous bacterial mechanism for ribosome rescue in the event of translation stalling. Although trans-translation is not essential in several bacterial species, it has been found essential for viability or virulence in a wide range of pathogens. We describe here that trans-translation is essential in the human pathogen Legionella pneumophila, the etiologic agent of Legionnaire's disease (LD), a severe form of nosocomial and community-acquired pneumonia. The ssrA gene coding for tmRNA, the key component of trans-translation, could not be deleted in L...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27829146/absence-of-non-histone-protein-complexes-at-natural-chromosomal-pause-sites-results-in-reduced-replication-pausing-in-aging-yeast-cells
#13
Marleny Cabral, Xin Cheng, Sukhwinder Singh, Andreas S Ivessa
There is substantial evidence that genomic instability increases during aging. Replication pausing (and stalling) at difficult-to-replicate chromosomal sites may induce genomic instability. Interestingly, in aging yeast cells, we observed reduced replication pausing at various natural replication pause sites (RPSs) in ribosomal DNA (rDNA) and non-rDNA locations (e.g., silent replication origins and tRNA genes). The reduced pausing occurs independent of the DNA helicase Rrm3p, which facilitates replication past these non-histone protein-complex-bound RPSs, and is independent of the deacetylase Sir2p...
November 8, 2016: Cell Reports
https://www.readbyqxmd.com/read/27827794/molecular-insights-into-protein-synthesis-with-proline-residues
#14
Sergey Melnikov, Justine Mailliot, Lukas Rigger, Sandro Neuner, Byung-Sik Shin, Gulnara Yusupova, Thomas E Dever, Ronald Micura, Marat Yusupov
Proline is an amino acid with a unique cyclic structure that facilitates the folding of many proteins, but also impedes the rate of peptide bond formation by the ribosome. As a ribosome substrate, proline reacts markedly slower when compared with other amino acids both as a donor and as an acceptor of the nascent peptide. Furthermore, synthesis of peptides with consecutive proline residues triggers ribosome stalling. Here, we report crystal structures of the eukaryotic ribosome bound to analogs of mono- and diprolyl-tRNAs...
December 2016: EMBO Reports
https://www.readbyqxmd.com/read/27821493/mechanistic-insights-into-mammalian-stress-granule-dynamics
#15
REVIEW
Marc D Panas, Pavel Ivanov, Paul Anderson
The accumulation of stalled translation preinitiation complexes (PICs) mediates the condensation of stress granules (SGs). Interactions between prion-related domains and intrinsically disordered protein regions found in SG-nucleating proteins promote the condensation of ribonucleoproteins into SGs. We propose that PIC components, especially 40S ribosomes and mRNA, recruit nucleators that trigger SG condensation. With resolution of stress, translation reinitiation reverses this process and SGs disassemble. By cooperatively modulating the assembly and disassembly of SGs, ribonucleoprotein condensation can influence the survival and recovery of cells exposed to unfavorable environmental conditions...
November 7, 2016: Journal of Cell Biology
https://www.readbyqxmd.com/read/27791127/cockayne-syndrome-group-a-and-b-proteins-converge-on-transcription-linked-resolution-of-non-b-dna
#16
Morten Scheibye-Knudsen, Anne Tseng, Martin Borch Jensen, Karsten Scheibye-Alsing, Evandro Fei Fang, Teruaki Iyama, Sanjay Kumar Bharti, Krisztina Marosi, Lynn Froetscher, Henok Kassahun, David Mark Eckley, Robert W Maul, Paul Bastian, Supriyo De, Soumita Ghosh, Hilde Nilsen, Ilya G Goldberg, Mark P Mattson, David M Wilson, Robert M Brosh, Myriam Gorospe, Vilhelm A Bohr
Cockayne syndrome is a neurodegenerative accelerated aging disorder caused by mutations in the CSA or CSB genes. Although the pathogenesis of Cockayne syndrome has remained elusive, recent work implicates mitochondrial dysfunction in the disease progression. Here, we present evidence that loss of CSA or CSB in a neuroblastoma cell line converges on mitochondrial dysfunction caused by defects in ribosomal DNA transcription and activation of the DNA damage sensor poly-ADP ribose polymerase 1 (PARP1). Indeed, inhibition of ribosomal DNA transcription leads to mitochondrial dysfunction in a number of cell lines...
November 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27791002/context-specific-inhibition-of-translation-by-ribosomal-antibiotics-targeting-the-peptidyl-transferase-center
#17
James Marks, Krishna Kannan, Emily J Roncase, Dorota Klepacki, Amira Kefi, Cédric Orelle, Nora Vázquez-Laslop, Alexander S Mankin
The first broad-spectrum antibiotic chloramphenicol and one of the newest clinically important antibacterials, linezolid, inhibit protein synthesis by targeting the peptidyl transferase center of the bacterial ribosome. Because antibiotic binding should prevent the placement of aminoacyl-tRNA in the catalytic site, it is commonly assumed that these drugs are universal inhibitors of peptidyl transfer and should readily block the formation of every peptide bond. However, our in vitro experiments showed that chloramphenicol and linezolid stall ribosomes at specific mRNA locations...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27784783/the-ribosome-restrains-molten-globule-formation-in-stalled-nascent-flavodoxin
#18
Joseline A Houwman, Estelle André, Adrie H Westphal, Willem J H van Berkel, Carlo P M van Mierlo
Folding of proteins usually involves intermediates, of which an important type is the molten globule (MG). MGs are ensembles of interconverting conformers that contain (non-)native secondary structure and lack the tightly packed tertiary structure of natively folded globular proteins. Whereas MGs of various purified proteins have been probed to date, no data are available on their presence and/or effect during protein synthesis. To study whether MGs arise during translation, we use ribosome-nascent chain (RNC) complexes of the electron transfer protein flavodoxin...
December 9, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27760805/the-minimum-open-reading-frame-aug-stop-induces-boron-dependent-ribosome-stalling-and-mrna-degradation
#19
Mayuki Tanaka, Naoyuki Sotta, Yusuke Yamazumi, Yui Yamashita, Kyoko Miwa, Katsunori Murota, Yukako Chiba, Masami Yokota Hirai, Tetsu Akiyama, Hitoshi Onouchi, Satoshi Naito, Toru Fujiwara
Upstream open reading frames (uORFs) are often translated ahead of the main ORF of a gene and regulate gene expression, sometimes in a condition-dependent manner, but such a role for the minimum uORF (hereafter referred to as AUG-stop) in living organisms is currently unclear. Here, we show that AUG-stop plays an important role in the boron (B)-dependent regulation of NIP5;1, encoding a boric acid channel required for normal growth under low B conditions in Arabidopsis thaliana High B enhanced ribosome stalling at AUG-stop, which was accompanied by the suppression of translation and mRNA degradation...
November 2016: Plant Cell
https://www.readbyqxmd.com/read/27758893/genome-wide-mapping-of-uncapped-and-cleaved-transcripts-reveals-a-role-for-the-nuclear-mrna-cap-binding-complex-in-cotranslational-rna-decay-in-arabidopsis
#20
Xiang Yu, Matthew R Willmann, Stephen J Anderson, Brian D Gregory
RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5' end to the 3' end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames...
October 2016: Plant Cell
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