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Ribosome profiling

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https://www.readbyqxmd.com/read/27924037/human-eif3b-and-eif3a-serve-as-the-nucleation-core-for-the-assembly-of-eif3-into-two-interconnected-modules-the-yeast-like-core-and-the-octamer
#1
Susan Wagner, Anna Herrmannová, Darina Šikrová, Leoš Shivaya Valášek
The 12-subunit mammalian eIF3 is the largest and most complex translation initiation factor and has been implicated in numerous steps of translation initiation, termination and ribosomal recycling. Imbalanced eIF3 expression levels are observed in various types of cancer and developmental disorders, but the consequences of altered eIF3 subunit expression on its overall structure and composition, and on translation in general, remain unclear. We present the first complete in vivo study monitoring the effects of RNAi knockdown of each subunit of human eIF3 on its function, subunit balance and integrity...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924019/a-ribosome-profiling-study-of-mrna-cleavage-by-the-endonuclease-rele
#2
Jae-Yeon Hwang, Allen R Buskirk
Implicated in persistence and stress response pathways in bacteria, RelE shuts down protein synthesis by cleaving mRNA within the ribosomal A site. Structural and biochemical studies have shown that RelE cuts with some sequence specificity, which we further characterize here, and that it shows no activity outside the context of the ribosome. We obtained a global view of the effect of RelE on translation by ribosome profiling, observing that ribosomes accumulate on the 5'-end of genes through dynamic cycles of mRNA cleavage, ribosome rescue and initiation...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923997/insights-into-the-mechanisms-of-eukaryotic-translation-gained-with-ribosome-profiling
#3
Dmitry E Andreev, Patrick B F O'Connor, Gary Loughran, Sergey E Dmitriev, Pavel V Baranov, Ivan N Shatsky
The development of Ribosome Profiling (RiboSeq) has revolutionized functional genomics. RiboSeq is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a 'snapshot' of ribosome positions at the transcriptome wide level. Although the method is predominantly used for analysis of differential gene expression and discovery of novel translated ORFs, the RiboSeq data can also be a rich source of information about molecular mechanisms of polypeptide synthesis and translational control...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923952/differences-in-the-nasopharyngeal-microbiome-during-acute-respiratory-tract-infection-with-human-rhinovirus-and-respiratory-syncytial-virus-in-infancy
#4
Christian Rosas-Salazar, Meghan H Shilts, Andrey Tovchigrechko, Seth Schobel, James D Chappell, Emma K Larkin, Jyoti Shankar, Shibu Yooseph, Karen E Nelson, Rebecca A Halpin, Martin L Moore, Larry J Anderson, R Stokes Peebles, Suman R Das, Tina V Hartert
Respiratory viruses alter the nasopharyngeal microbiome and may be associated with a distinct microbial signature. To test this hypothesis, we compared the nasopharyngeal microbiome of 135 previously healthy infants with acute respiratory infection due to human rhinovirus (HRV; n = 52) or respiratory syncytial virus (RSV; n = 83). The nasopharyngeal microbiome was assessed by sequencing the V4 region of the 16S ribosomal RNA. Respiratory viruses were identified by quantitative reverse-transcription polymerase chain reaction...
December 15, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27909995/solithromycin-a-novel-fluoroketolide-for-the-treatment-of-community-acquired-bacterial-pneumonia
#5
REVIEW
George G Zhanel, Erika Hartel, Heather Adam, Sheryl Zelenitsky, Michael A Zhanel, Alyssa Golden, Frank Schweizer, Bala Gorityala, Philippe R S Lagacé-Wiens, Andrew J Walkty, Alfred S Gin, Daryl J Hoban, Joseph P Lynch, James A Karlowsky
Solithromycin is a novel fluoroketolide developed in both oral and intravenous formulations to address increasing macrolide resistance in pathogens causing community-acquired bacterial pneumonia (CABP). When compared with its macrolide and ketolide predecessors, solithromycin has several structural modifications which increase its ribosomal binding and reduce its propensity to known macrolide resistance mechanisms. Solithromycin, like telithromycin, affects 50S ribosomal subunit formation and function, as well as causing frame-shift errors during translation...
December 1, 2016: Drugs
https://www.readbyqxmd.com/read/27909306/rpl5-on-1p22-1-is-recurrently-deleted-in-multiple-myeloma-and-its-expression-is-linked-to-bortezomib-response
#6
I J F Hofman, M Van Duin, E De Bruyne, L Fancello, G Mulligan, E Geerdens, E Garelli, C Mancini, H Lemmens, M Delforge, P Vandenberghe, I Wlodarska, A Aspesi, L Michaux, K Vanderkerken, P Sonneveld, K De Keersmaecker
Chromosomal region 1p22 is deleted in ⩾20% of multiple myeloma (MM) patients, suggesting the presence of an unidentified tumor suppressor. Using high-resolution genomic profiling, we delimit a 58 kb minimal deleted region (MDR) on 1p22.1 encompassing two genes: ectopic viral integration site 5 (EVI5) and ribosomal protein L5 (RPL5). Low mRNA expression of EVI5 and RPL5 was associated with worse survival in diagnostic cases. Patients with 1p22 deletion had lower mRNA expression of EVI5 and RPL5, however, 1p22 deletion status is a bad predictor of RPL5 expression in some cases, suggesting that other mechanisms downregulate RPL5 expression...
December 2, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27908735/unr-csde1-drives-a-post-transcriptional-program-to-promote-melanoma-invasion-and-metastasis
#7
Laurence Wurth, Panagiotis Papasaikas, David Olmeda, Nadine Bley, Guadalupe T Calvo, Santiago Guerrero, Daniela Cerezo-Wallis, Javier Martinez-Useros, María García-Fernández, Stefan Hüttelmaier, Maria S Soengas, Fátima Gebauer
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination...
November 14, 2016: Cancer Cell
https://www.readbyqxmd.com/read/27902881/the-chimeric-nature-of-the-genomes-of-marine-magnetotactic-coccoid-ovoid-bacteria-defines-a-novel-group-of-proteobacteria
#8
Boyang Ji, Sheng-Da Zhang, Wei-Jia Zhang, Zoe Rouy, François Alberto, Claire-Lise Santini, Sophie Mangenot, Séverine Gagnot, Nadège Philippe, Nathalie Pradel, Lichen Zhang, Sébastien Tempel, Ying Li, Claudine Médigue, Bernard Henrissat, Pedro M Coutinho, Valérie Barbe, Emmanuel Talla, Long-Fei Wu
Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared to other bacterial taxonomic groups remain to be illustrated. Here, we analyzed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1...
November 30, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27902365/the-oral-cavities-of-healthy-infants-harbor-high-proportions-of-streptococcus-salivarius-strains-with-phenotypic-and-genotypic-resistance-to-multiple-classes-of-antibiotics
#9
Thaís H Palma, Erika Harth-Chú, Jodie Scott, Rafael N Stipp, Heike Boisvert, Mariana F Salomão, Jéssica D Theobaldo, Rosana F Possobon, Leandro C Nascimento, Jonathan W McCafferty, Lina Faller, Margaret J Duncan, Renata O Mattos-Graner
Emerging antibiotic resistance in the oropharyngeal microbiota, of which Streptococcus salivarius is a prominent species, represents a challenge for treating pediatric populations. In this study, we investigated the role of S. salivarius as a reservoir for antibiotic resistance genes (ARG) in the oral microbiota by analyzing 95 S. salivarius isolates from 22 healthy infants (2 to 16 months of age). Minimum inhibitory concentrations (MIC) of penicillin G, amoxicillin, erythromycin, tetracycline, doxycycline and streptomycin were determined...
October 24, 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27899360/widespread-and-dynamic-translational-control-of-red-blood-cell-development
#10
Juan R Alvarez-Dominguez, Xu Zhang, Wenqian Hu
Cell development requires tight yet dynamic control of protein production. Here, we use parallel RNA and ribosome profiling to study translational regulatory dynamics during murine terminal erythropoiesis. We uncover pervasive translational control of protein synthesis, including widespread alternative translation initiation and termination, robust discrimination of long non-coding from micropeptide-encoding RNAs, and dynamic use of upstream reading frames. We further identify hundreds of mRNAs whose translation efficiency is dynamically controlled during erythropoiesis, and find that they enrich for target sites of RNA-binding proteins that are hematopoietic cell-specific, thus unraveling potential regulators of erythroid translational programs...
November 29, 2016: Blood
https://www.readbyqxmd.com/read/27895634/cytosolic-proteome-profiling-of-aminoglycosides-resistant-mycobacterium-tuberculosis-clinical-isolates-using-maldi-tof-ms
#11
Divakar Sharma, Manju Lata, Rananjay Singh, Nirmala Deo, Krishnamurthy Venkatesan, Deepa Bisht
Emergence of extensively drug resistant tuberculosis (XDR-TB) is the consequence of the failure of second line TB treatment. Aminoglycosides are the important second line anti-TB drugs used to treat the multi drug resistant tuberculosis (MDR-TB). Main known mechanism of action of aminoglycosides is to inhibit the protein synthesis by inhibiting the normal functioning of ribosome. Primary target of aminoglycosides are the ribosomal RNA and its associated proteins. Various mechanisms have been proposed for aminoglycosides resistance but still some are unsolved...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27894252/transcriptome-analysis-reveals-the-genetic-basis-underlying-the-seasonal-development-of-keratinized-nuptial-spines-in-leptobrachium-boringii
#12
Wei Zhang, Yue Guo, Jun Li, Li Huang, Eric Gilbert Kazitsa, Hua Wu
BACKGROUND: The expression of sexually selected traits often varies with populations' breeding cycles in many animals. The elucidation of mechanisms underlying the expression of such traits is a research topic in evolutionary biology; however, the genetic basis of the seasonal development of their expression remains unknown. Male Leptobrachium boringii develop keratinized nuptial spines on their upper jaw during the breeding season that fall off when the breeding season ends. To illuminate the genetic basis for the expression of this trait and its seasonal development, we assessed the de novo transcriptome for L...
November 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27885668/characterization-of-gambierdiscus-lapillus-sp-nov-gonyaulacales-dinophyceae-a-new-toxic-dinoflagellate-from-the-great-barrier-reef-australia
#13
Anna Liza Kretzschmar, Arjun Verma, D Tim Harwood, Mona Hoppenrath, Shauna Murray
Gambierdiscus is a genus of benthic dinoflagellates found worldwide. Some species produce neurotoxins (maitotoxins and ciguatoxins) which bioaccumulate and cause ciguatera fish poisoning, a potentially fatal food-borne illness that is common worldwide in tropical regions. The investigation of toxigenic species of Gambierdiscus in ciguatera fish poisoning endemic regions in Australia is necessary as a first step in order to determine which species of Gambierdiscus are related to ciguatera fish poisoning cases occurring in this region...
November 25, 2016: Journal of Phycology
https://www.readbyqxmd.com/read/27884202/extending-colonic-mucosal-microbiome-analysis-assessment-of-colonic-lavage-as-a-proxy-for-endoscopic-colonic-biopsies
#14
Euan Watt, Matthew R Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I Murray, Emad El-Omar, Georgina L Hold
BACKGROUND: Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size...
November 25, 2016: Microbiome
https://www.readbyqxmd.com/read/27884106/spectre-a-spectral-coherence-based-classifier-of-actively-translated-transcripts-from-ribosome-profiling-sequence-data
#15
Sang Y Chun, Caitlin M Rodriguez, Peter K Todd, Ryan E Mills
BACKGROUND: Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Prevailing analytical approaches applied to this technology make use of sequence fragment length profiling or reading frame occupancy enrichment to differentiate between active translation and background noise, however they do not consider additional characteristics inherent to the technology which limits their overall accuracy. RESULTS: Here, we present an analytical tool that models the overall tri-nucleotide periodicity of ribosomal occupancy using a classifier based on spectral coherence...
November 25, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27881780/negative-allosteric-modulation-of-mglur5-partially-corrects-pathophysiology-in-a-mouse-model-of-rett-syndrome
#16
Jifang Tao, Hao Wu, Amanda A Coronado, Elizabeth de Laittre, Emily K Osterweil, Yi Zhang, Mark F Bear
: Rett syndrome (RTT) is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MECP2), an epigenetic regulator of mRNA transcription. Here, we report a test of the hypothesis of shared pathophysiology of RTT and fragile X, another monogenic cause of autism and intellectual disability. In fragile X, the loss of the mRNA translational repressor FMRP leads to exaggerated protein synthesis downstream of metabotropic glutamate receptor 5 (mGluR5). We found that mGluR5- and protein-synthesis-dependent synaptic plasticity were similarly altered in area CA1 of Mecp2 KO mice...
November 23, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27880005/s-nitrosoglutathione-promotes-cell-wall-remodelling-alters-the-transcriptional-profile-and-induces-root-hair-formation-in-the-hairless-root-hair-defective-6-rhd6-mutant-of-arabidopsis-thaliana
#17
Camila Fernandes Moro, Marilia Gaspar, Felipe Rodrigues da Silva, Sivakumar Pattathil, Michael G Hahn, Ione Salgado, Marcia Regina Braga
Nitric oxide (NO) exerts pleiotropic effects on plant development; however, its involvement in cell wall modification during root hair formation (RHF) has not yet been addressed. Here, mutants of Arabidopsis thaliana with altered root hair phenotypes were used to assess the involvement of S-nitrosoglutathione (GSNO), the primary NO source, in cell wall dynamics and gene expression in roots induced to form hairs. GSNO and auxin restored the root hair phenotype of the hairless root hair defective 6 (rhd6) mutant...
November 23, 2016: New Phytologist
https://www.readbyqxmd.com/read/27878588/the-impact-of-erdosteine-on-cisplatin-induced-ototoxicity-a-proteomics-approach
#18
Sofia Waissbluth, Delphine Garnier, Olubunmi V Akinpelu, Pezhman Salehi, Sam J Daniel
Cisplatin is a commonly used chemotherapeutic agent and causes serious side effects, including progressive and irreversible hearing loss. No treatment is currently available for cisplatin-induced ototoxicity. We have previously demonstrated that erdosteine, a potent antioxidant, partially protected the cochlea against cisplatin toxicity in vivo. The aims of this study were to (1) evaluate the protein profiles of the cochlea following cisplatin administration and (2) evaluate the impact of erdosteine on the protein profile using a proteomics-based approach...
November 23, 2016: European Archives of Oto-rhino-laryngology
https://www.readbyqxmd.com/read/27875984/plastid-nucleotide-resolution-analysis-of-next-generation-sequencing-and-genomics-data
#19
Joshua G Dunn, Jonathan S Weissman
BACKGROUND: Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments - for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length - analytical tools are often required to extract the biological meaning from the alignments before analysis...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27873260/label-free-quantitation-of-ribosomal-proteins-from-bacillus-subtilis-for-antibiotic-research
#20
Sina Schäkermann, Pascal Prochnow, Julia E Bandow
Current research is focusing on ribosome heterogeneity as a response to changing environmental conditions and stresses, such as antibiotic stress. Altered stoichiometry and composition of ribosomal proteins as well as association of additional protein factors are mechanisms for shaping the protein expression profile or hibernating ribosomes. Here, we present a method for the isolation of ribosomes to analyze antibiotic-induced changes in the composition of ribosomes in Bacillus subtilis or other bacteria. Ribosomes and associated proteins are isolated by ultracentrifugation and proteins are identified and quantified using label-free mass spectrometry...
2017: Methods in Molecular Biology
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