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Ribosome profiling

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https://www.readbyqxmd.com/read/28812548/bacteroidales-recruit-il-6-producing-intraepithelial-lymphocytes-in-the-colon-to-promote-barrier-integrity
#1
K A Kuhn, H M Schulz, E H Regner, E L Severs, J D Hendrickson, G Mehta, A K Whitney, D Ir, N Ohri, C E Robertson, D N Frank, E L Campbell, S P Colgan
Interactions between the microbiota and distal gut are important for the maintenance of a healthy intestinal barrier; dysbiosis of intestinal microbial communities has emerged as a likely contributor to diseases that arise at the level of the mucosa. Intraepithelial lymphocytes (IELs) are positioned within the epithelial barrier, and in the small intestine they function to maintain epithelial homeostasis. We hypothesized that colon IELs promote epithelial barrier function through the expression of cytokines in response to interactions with commensal bacteria...
August 16, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28808330/generation-and-characterization-of-a-mouse-line-for-monitoring-translation-in-dopaminergic-neurons
#2
Joseph D Dougherty
We developed a mouse line targeting midbrain dopamine neurons for Translating Ribosome Affinity Purification(TRAP). Here, we briefly report on the basic characterization of this mouse line including confirmation of expression of the transgene in midbrain dopamine neurons and validation of its effectiveness in capturing mRNA from these cells. We also report a translational profile of these neurons which may be of use to investigators studying the gene expression of these cells. Finally, we have provided the line to Jackson Laboratories for distribution and use in future studies...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808135/mutations-in-eif5b-confer-thermosensitive-and-pleiotropic-phenotypes-via-translation-defects-in-arabidopsis-thaliana
#3
Liyuan Zhang, Xinye Liu, Kishor Gaikwad, Xiaoxia Kou, Fei Wang, Xuejun Tian, Mingming Xin, Zhongfu Ni, Qixin Sun, Huiru Peng, Elizabeth Vierling
The conserved eukaryotic translation initiation factor 5B, eIF5B, is a GTPase that acts late in translation initiation. We found that an Arabidopsis thaliana mutant sensitive to hot temperatures 3 (hot3-1), which behaves as wild type in the absence of stress but is unable to acclimate to high temperature, carries a missense mutation in eIF5B1 gene (At1g76810),, producing a temperature sensitive protein. A more severe, T-DNA insertion allele (hot3-2) causes pleiotropic developmental phenotypes. Surprisingly, Arabidopsis has three other eIF5B genes that do not substitute for eIF5B1; two of these appear to be in the process of pseudogenization...
August 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28807055/transcriptomic-profiling-of-microbe-microbe-interactions-reveals-the-specific-response-of-the-biocontrol-strain-p-fluorescens-in5-to-the-phytopathogen-rhizoctonia-solani
#4
Rosanna C Hennessy, Mikkel A Glaring, Stefan Olsson, Peter Stougaard
BACKGROUND: Few studies to date report the transcriptional response of biocontrol bacteria toward phytopathogens. In order to gain insights into the potential mechanism underlying the antagonism of the antimicrobial producing strain P. fluorescens In5 against the phytopathogens Rhizoctonia solani and Pythium aphanidermatum, global RNA sequencing was performed. METHODS: Differential gene expression profiling of P. fluorescens In5 in response to either R. solani or P...
August 10, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28797234/succinyl-proteome-profiling-of-dendrobium-officinale-an-important-traditional-chinese-orchid-herb-revealed-involvement-of-succinylation-in-the-glycolysis-pathway
#5
Shangguo Feng, Kaili Jiao, Hong Guo, Mengyi Jiang, Juan Hao, Huizhong Wang, Chenjia Shen
BACKGROUND: Lysine succinylation is a ubiquitous and important protein post-translational modification in various eukaryotic and prokaryotic cells. However, its functions in Dendrobium officinale, an important traditional Chinese orchid herb with high polysaccharide contents, are largely unknown. RESULTS: In our study, LC-MS/MS was used to identify the peptides that were enriched by immune-purification with a high-efficiency succinyl-lysine antibody. In total, 314 lysine succinylation sites in 207 proteins were identified...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28791303/the-us8-us4-es31-and-ul14-ribosomal-protein-genes-are-dysregulated-in-nasopharyngeal-carcinoma-cell-lines
#6
Edmund Ui-Hang Sim, Kher-Lee Ng, Choon-Weng Lee, Kumaran Narayanan
The association of ribosomal proteins with carcinogenesis of nasopharyngeal carcinoma (NPC) has been established in a limited subset of ribosomal protein genes. To date, three ribosomal protein genes, eL27 (L27), eL41 (L41), and eL43 (L37a), have been found to be differentially expressed in cell lines derived from NPC tumors. This raises the possibility of more ribosomal protein genes that could be associated with NPC. In this study, we investigated the expression profiles of eight ribosomal protein genes, uS8 (S8), uS4 (S9), eS31 (S27a), eL6 (L6), eL18 (L18), uL14 (L23), eL24 (L24), and eL30 (L30), in six NPC-derived cell lines (HONE-1, SUNE1, HK1, TW01, TW04, and C666-1)...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28790420/comparative-transcriptional-profiling-of-tildipirosin-resistant-and-sensitive-haemophilus-parasuis
#7
Zhixin Lei, Shulin Fu, Bing Yang, Qianying Liu, Saeed Ahmed, Lei Xu, Jincheng Xiong, Jiyue Cao, Yinsheng Qiu
Numerous studies have been conducted to examine the molecular mechanism of Haemophilus parasuis resistance to antibiotic, but rarely to tildipirosin. In the current study, transcriptional profiling was applied to analyse the variation in gene expression of JS0135 and tildipirosin-resistant JS32. The growth curves showed that JS32 had a higher growth rate but fewer bacteria than JS0135. The cell membranes of JS32 and a resistant clinical isolate (HB32) were observed to be smoother than those of JS0135. From the comparative gene expression profile 349 up- and 113 downregulated genes were observed, covering 37 GO and 63 KEGG pathways which are involved in biological processes (11), cellular components (17), molecular function (9), cellular processes (1), environmental information processing (4), genetic information processing (9) and metabolism (49) affected in JS32...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28780152/functional-genomic-exploration-reveals-that-ss-riok-1-is-essential-for-the-development-and-survival-of-strongyloides-stercoralis-larvae
#8
Wang Yuan, Huan Zhou, James B Lok, Weiqiang Lei, Siyuan He, Robin B Gasser, Rui Zhou, Rui Fang, Yanqin Zhou, Junlong Zhao, Min Hu
Protein kinase RIOK-1 is a non-ribosomal factor essential for rRNA cleavage and ribosome small subunit maturation. It is encoded in all eukaryotic organisms. The RIOK-1 encoding gene of Caenorhabditis elegans (Ce-riok-1) is expressed in the neuronal and reproductive systems in larvae and adults of this free-living nematode, and it supports larval growth and development of the adult gonad. In spite of its recognised roles in model organisms such as C. elegans, little is known about the function of this molecule in parasitic nematodes...
August 3, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28777931/biallelic-mutations-in-mrps34-lead-to-instability-of-the-small-mitoribosomal-subunit-and-leigh-syndrome
#9
Nicole J Lake, Bryn D Webb, David A Stroud, Tara R Richman, Benedetta Ruzzenente, Alison G Compton, Hayley S Mountford, Juliette Pulman, Coralie Zangarelli, Marlene Rio, Nathalie Bodaert, Zahra Assouline, Mingma D Sherpa, Eric E Schadt, Sander M Houten, James Byrnes, Elizabeth M McCormick, Zarazuela Zolkipli-Cunningham, Katrina Haude, Zhancheng Zhang, Kyle Retterer, Renkui Bai, Sarah E Calvo, Vamsi K Mootha, John Christodoulou, Agnes Rötig, Aleksandra Filipovska, Ingrid Cristian, Marni J Falk, Metodi D Metodiev, David R Thorburn
The synthesis of all 13 mitochondrial DNA (mtDNA)-encoded protein subunits of the human oxidative phosphorylation (OXPHOS) system is carried out by mitochondrial ribosomes (mitoribosomes). Defects in the stability of mitoribosomal proteins or mitoribosome assembly impair mitochondrial protein translation, causing combined OXPHOS enzyme deficiency and clinical disease. Here we report four autosomal-recessive pathogenic mutations in the gene encoding the small mitoribosomal subunit protein, MRPS34, in six subjects from four unrelated families with Leigh syndrome and combined OXPHOS defects...
August 3, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28776098/transcriptome-analysis-of-the-thermotolerant-yeast-kluyveromyces-marxianus-cct-7735-under-ethanol-stress
#10
Raphael Hermano Santos Diniz, Juan C Villada, Mariana Caroline Tocantins Alvim, Pedro Marcus Pereira Vidigal, Nívea Moreira Vieira, Mónica Lamas-Maceiras, María Esperanza Cerdán, María-Isabel González-Siso, Petri-Jaan Lahtvee, Wendel Batista da Silveira
The thermotolerant yeast Kluyveromyces marxianus displays a potential to be used for ethanol production from both whey and lignocellulosic biomass at elevated temperatures, which is highly alluring to reduce the cost of the bioprocess. Nevertheless, contrary to Saccharomyces cerevisiae, K. marxianus cannot tolerate high ethanol concentrations. We report the transcriptional profile alterations in K. marxianus under ethanol stress in order to gain insights about mechanisms involved with ethanol response. Time-dependent changes have been characterized under the exposure of 6% ethanol and compared with the unstressed cells prior to the ethanol addition...
August 3, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28772121/cell-type-specific-translation-profiling-reveals-a-novel-strategy-for-treating-fragile-x-syndrome
#11
Sophie R Thomson, Sang S Seo, Stephanie A Barnes, Susana R Louros, Melania Muscas, Owen Dando, Caoimhe Kirby, David J A Wyllie, Giles E Hardingham, Peter C Kind, Emily K Osterweil
Excessive mRNA translation downstream of group I metabotropic glutamate receptors (mGlu1/5) is a core pathophysiology of fragile X syndrome (FX); however, the differentially translating mRNAs that contribute to altered neural function are not known. We used translating ribosome affinity purification (TRAP) and RNA-seq to identify mistranslating mRNAs in CA1 pyramidal neurons of the FX mouse model (Fmr1(-/y)) hippocampus, which exhibit exaggerated mGlu1/5-induced long-term synaptic depression (LTD). In these neurons, we find that the Chrm4 transcript encoding muscarinic acetylcholine receptor 4 (M4) is excessively translated, and synthesis of M4 downstream of mGlu5 activation is mimicked and occluded...
August 2, 2017: Neuron
https://www.readbyqxmd.com/read/28763796/the-metabolic-regulator-mtorc1-controls-terminal-myeloid-differentiation
#12
Pui Y Lee, David B Sykes, Sarah Ameri, Demetrios Kalaitzidis, Julia F Charles, Nathan Nelson-Maney, Kevin Wei, Pierre Cunin, Allyn Morris, Astrid E Cardona, David E Root, David T Scadden, Peter A Nigrovic
Monocytes are derived from hematopoietic stem cells through a series of intermediate progenitor stages, but the factors that regulate this process are incompletely defined. Using a Ccr2/Cx3cr1 dual-reporter system to model murine monocyte ontogeny, we conducted a small-molecule screen that identified an essential role of mechanistic target of rapamycin complex 1 (mTORC1) in the development of monocytes and other myeloid cells. Confirmatory studies using mice with inducible deletion of the mTORC1 component Raptor demonstrated absence of mature circulating monocytes, as well as disruption in neutrophil and dendritic cell development, reflecting arrest of terminal differentiation at the granulocyte-monocyte progenitor stage...
May 26, 2017: Science Immunology
https://www.readbyqxmd.com/read/28763019/use-of-antibiotics-for-maintenance-of-axenic-cultures-of-amphidinium-carterae-for-the-analysis-of-translation
#13
Chieh-Lun Liu, Allen R Place, Rosemary Jagus
Most dinoflagellates in culture are bacterized, complicating the quantification of protein synthesis, as well as the analysis of its regulation. In bacterized cultures of Amphidinium carterae Hulbert, up to 80% of protein synthetic activity appears to be predominantly bacterial based on responses to inhibitors of protein synthesis. To circumvent this, axenic cultures of A. carterae were obtained and shown to respond to inhibitors of protein synthesis in a manner characteristic of eukaryotes. However, these responses changed with time in culture correlating with the reappearance of bacteria...
August 1, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28761783/quantitative-real-time-pcr-analysis-of-anopheles-dirus-tep1-and-nos-during-plasmodium-berghei-infection-using-three-reference-genes
#14
Jonathan W K Liew, Mun Yik Fong, Yee Ling Lau
Quantitative reverse transcription PCR (qRT-PCR) has been an integral part of characterizing the immunity of Anopheles mosquitoes towards Plasmodium invasion. Two anti-Plasmodium factors of Anopheles, thioester-containing protein 1 (TEP1) and nitric oxide synthase (NOS), play a role in the refractoriness of Anopheles towards Plasmodium infection and are generally expressed during infection. However, these are less studied in Anopheles dirus, a dominant malaria vector in Southeast Asia. Furthermore, most studies used a single reference gene for normalization during gene expression analysis without proper validation...
2017: PeerJ
https://www.readbyqxmd.com/read/28759167/titsmall-but-mighty-functional-peptides-encoded-by-small-orfs-in-plants
#15
REVIEW
Polly Yingshan Hsu, Philip N Benfey
Peptides encoded by small open reading frames (sORFs, usually < 100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from non-translated ones. Here we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics...
July 31, 2017: Proteomics
https://www.readbyqxmd.com/read/28757607/ubiquitination-of-stalled-ribosome-triggers-ribosome-associated-quality-control
#16
Yoshitaka Matsuo, Ken Ikeuchi, Yasushi Saeki, Shintaro Iwasaki, Christian Schmidt, Tsuyoshi Udagawa, Fumiya Sato, Hikaru Tsuchiya, Thomas Becker, Keiji Tanaka, Nicholas T Ingolia, Roland Beckmann, Toshifumi Inada
Translation arrest by polybasic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. Here we report that ubiquitination of the 40S ribosomal protein uS10 by the E3 ubiquitin ligase Hel2 (or RQT1) is required for RQC. We identify a RQC-trigger (RQT) subcomplex composed of the RNA helicase-family protein Slh1/Rqt2, the ubiquitin-binding protein Cue3/Rqt3, and yKR023W/Rqt4 that is required for RQC. The defects in RQC of the RQT mutants correlate with sensitivity to anisomycin, which stalls ribosome at the rotated form...
July 31, 2017: Nature Communications
https://www.readbyqxmd.com/read/28757599/different-metabolic-pathways-are-involved-in-response-of-saccharomyces-cerevisiae-to-l-a-and-m-viruses
#17
Juliana Lukša, Bazilė Ravoitytė, Aleksandras Konovalovas, Lina Aitmanaitė, Anzhelika Butenko, Vyacheslav Yurchenko, Saulius Serva, Elena Servienė
Competitive and naturally occurring yeast killer phenotype is governed by coinfection with dsRNA viruses. Long-term relationship between the host cell and viruses appear to be beneficial and co-adaptive; however, the impact of viral dsRNA on the host gene expression has barely been investigated. Here, we determined the transcriptomic profiles of the host Saccharomyces cerevisiae upon the loss of the M-2 dsRNA alone and the M-2 along with the L-A-lus dsRNAs. We provide a comprehensive study based on the high-throughput RNA-Seq data, Gene Ontology and the analysis of the interaction networks...
July 25, 2017: Toxins
https://www.readbyqxmd.com/read/28754723/a-functional-link-between-bir1-and-the-saccharomyces-cerevisiae-ctf19-kinetochore-complex-revealed-through-quantitative-fitness-analysis
#18
Vasso Makrantoni, Adam Ciesiolka, Conor Lawless, Josefin Fernius, Adele Marston, David Lydall, Michael J R Stark
The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15) and two additional proteins (Survivin/Bir1 and Borealin/Nbl1). Here we report a genome-wide genetic interaction screen in Saccharomyces cerevisiae using the bir1-17 mutant, identifying through quantitative fitness analysis deletion mutations that act as enhancers and suppressors. Gene knockouts affecting the Ctf19 kinetochore complex were identified as the strongest enhancers of bir1-17, while mutations affecting the large ribosomal subunit or the mRNA nonsense-mediated decay (NMD) pathway caused strong phenotypic suppression...
July 28, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28747643/generation-of-ribosome-imprinted-polymers-for-sensitive-detection-of-translational-responses
#19
Helen A King, Hazim F El-Sharif, Ana M Matia-González, Valentina Iadevaia, Adeola Fowotade, Subrayal M Reddy, André P Gerber
Whilst the profiling of the transcriptome and proteome even of single-cells becomes feasible, the analysis of the translatome, which refers to all messenger RNAs (mRNAs) engaged with ribosomes for protein synthesis, is still an elaborate procedure requiring millions of cells. Herein, we report the generation and use of "smart materials", namely molecularly imprinted polymers (MIPs) to facilitate the isolation of ribosomes and translated mRNAs from merely 1,000 cells. In particular, we show that a hydrogel-based ribosome imprinted polymer could recover ribosomes and associated mRNAs from human, simian and mice cellular extracts, but did not selectively enrich yeast ribosomes, thereby demonstrating selectivity...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28745585/maturation-of-selected-human-mitochondrial-trnas-requires-deadenylation
#20
Sarah F Pearce, Joanna Rorbach, Lindsey Van Haute, Aaron R D'Souza, Pedro Rebelo-Guiomar, Christopher A Powell, Ian Brierley, Andrew E Firth, Michal Minczuk
Human mitochondria contain a genome (mtDNA) that encodes essential subunits of the oxidative phosphorylation system. Expression of mtDNA entails multi-step maturation of precursor RNA. In other systems, the RNA life cycle involves surveillance mechanisms, however, the details of RNA quality control have not been extensively characterised in human mitochondria. Using a mitochondrial ribosome profiling and mitochondrial poly(A)-tail RNA sequencing (MPAT-Seq) assay, we identify the poly(A)-specific exoribonuclease PDE12 as a major factor for the quality control of mitochondrial non-coding RNAs...
July 26, 2017: ELife
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