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Ribosome profiling

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https://www.readbyqxmd.com/read/28091612/ribosome-profiling-guided-depletion-of-an-mrna-increases-cell-growth-rate-and-protein-secretion
#1
Thomas Beuchert Kallehauge, Shangzhong Li, Lasse Ebdrup Pedersen, Tae Kwang Ha, Daniel Ley, Mikael Rørdam Andersen, Helene Faustrup Kildegaard, Gyun Min Lee, Nathan E Lewis
Recombinant protein production coopts the host cell machinery to provide high protein yields of industrial enzymes or biotherapeutics. However, since protein translation is energetically expensive and tightly controlled, it is unclear if highly expressed recombinant genes are translated as efficiently as host genes. Furthermore, it is unclear how the high expression impacts global translation. Here, we present the first genome-wide view of protein translation in an IgG-producing CHO cell line, measured with ribosome profiling...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28089629/a-rack1-like-protein-regulates-hyphal-morphogenesis-root-entry-and-in-vivo-virulence-in-verticillium-dahlia
#2
Lei Yuan, Yaxin Su, Shuai Zhou, Yigao Feng, Wangzhen Guo, Xinyu Wang
To identify key genes expressed in Verticillium dahliae in early stages of infection of cotton roots, spore suspensions of eight V. dahliae isolates with different virulence levels were induced by cotton roots and genes expressed in these isolates during the early stages of infection were profiled. A gene that was differentially expressed between highly and less virulent strains was identified. Cloning and bioinformatics analysis of the gene suggested that it belongs to the putative Gβ-like/RACK1 protein family, and has seven WD40 domains...
January 9, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28079881/translational-upregulation-of-aurora-a-by-hnrnp-q1-contributes-to-cell-proliferation-and-tumorigenesis-in-colorectal-cancer
#3
Chien-Hsien Lai, Yu-Chuan Huang, Jenq-Chang Lee, Joseph Ta-Chien Tseng, Kung-Chao Chang, Yen-Ju Chen, Nai-Jhu Ding, Pao-Hsuan Huang, Wen-Chang Chang, Bo-Wen Lin, Ruo-Yu Chen, Yu-Chu Wang, Yi-Chien Lai, Liang-Yi Hung
By using RNA-immunoprecipitation assay following next-generation sequencing, a group of cell cycle-related genes targeted by hnRNP Q1 were identified, including Aurora-A kinase. Overexpressed hnRNP Q1 can upregulate Aurora-A protein, but not alter the mRNA level, through enhancing the translational efficiency of Aurora-A mRNA, either in a cap-dependent or -independent manner, by interacting with the 5'-UTR of Aurora-A mRNA through its RNA-binding domains (RBDs) 2 and 3. By ribosomal profiling assay further confirmed the translational regulation of Aurora-A mRNA by hnRNP Q1...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28077873/translation-from-unconventional-5-start-sites-drives-tumour-initiation
#4
Ataman Sendoel, Joshua G Dunn, Edwin H Rodriguez, Shruti Naik, Nicholas C Gomez, Brian Hurwitz, John Levorse, Brian D Dill, Daniel Schramek, Henrik Molina, Jonathan S Weissman, Elaine Fuchs
We are just beginning to understand how translational control affects tumour initiation and malignancy. Here we use an epidermis-specific, in vivo ribosome profiling strategy to investigate the translational landscape during the transition from normal homeostasis to malignancy. Using a mouse model of inducible SOX2, which is broadly expressed in oncogenic RAS-associated cancers, we show that despite widespread reductions in translation and protein synthesis, certain oncogenic mRNAs are spared. During tumour initiation, the translational apparatus is redirected towards unconventional upstream initiation sites, enhancing the translational efficiency of oncogenic mRNAs...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28073836/ionotropic-glutamate-receptors-activate-cell-signaling-in-response-to-glutamate-in-schwann-cells
#5
Wendy M Campana, Elisabetta Mantuano, Pardis Azmoon, Kenneth Henry, Michael A Banki, John H Kim, Donald P Pizzo, Steven L Gonias
In the peripheral nervous system, Schwann cells (SCs) demonstrate surveillance activity, detecting injury and undergoing trans-differentiation to support repair. SC receptors that detect peripheral nervous system injury remain incompletely understood. We used RT-PCR to profile ionotropic glutamate receptor expression in cultured SCs. We identified subunits required for assembly of N-methyl-d-aspartic acid (NMDA) receptors (NMDA-R), α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors, and kainate receptors...
January 10, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28073547/morphology-molecular-phylogeny-and-azaspiracid-profile-of-azadinium-poporum-dinophyceae-from-the-gulf-of-mexico
#6
REVIEW
Zhaohe Luo, Bernd Krock, Kenneth Neil Mertens, Andrea Michelle Price, Robert Eugene Turner, Nancy N Rabalais, Haifeng Gu
Azadinium poporum produces a variety of azaspiracids and consists of several ribotypes, but information on its biogeography is limited. A strain of A. poporum (GM29) was incubated from a Gulf of Mexico sediment sample. Strain GM29 was characterized by a plate pattern of po, cp, x, 4', 3a, 6″, 6C, 5S, 6‴, 2⁗, a distinct ventral pore at the junction of po and the first two apical plates, and a lack of an antapical spine, thus fitting the original description of A. poporum. The genus Azadinium has not been reported in waters of the United States of America before this study...
May 2016: Harmful Algae
https://www.readbyqxmd.com/read/28065880/complete-genome-sequence-and-expression-profile-of-the-commercial-lytic-enzyme-producer-lysobacter-enzymogenes-m497-1
#7
Hideto Takami, Atsushi Toyoda, Ikuo Uchiyama, Takehiko Itoh, Yoshihiro Takaki, Wataru Arai, Shinro Nishi, Mikihiko Kawai, Kazuo Shin-Ya, Haruo Ikeda
Lysobacter enzymogenes M497-1 is a producer of commercialized achromopeptidase and is expected to harbour genes encoding various other antimicrobial enzymes. Here, we present the complete sequence of the genome of M497-1 and the expression profiles of the genes for various antimicrobial enzymes. Of the 117 peptidase-encoding genes found in the 6.1-Mb genome of M497-1, 15 genes (aside from the gene encoding the achromopeptidase) were expressed at a level higher than that of the average ribosomal protein genes in the 24-h culture...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28062796/integrated-cellular-and-plasma-proteomics-of-contrasting-b-cell-cancers-reveals-common-unique-and-systemic-signatures
#8
Harvey E Johnston, Matthew J Carter, Kerry L Cox, Melanie Dunscombe, Antigoni Manousopoulou, Paul A Townsend, Spiro D Garbis, Mark S Cragg
Approximately 800,000 leukaemia and lymphoma cases are diagnosed worldwide each year. Burkitt's lymphoma (BL) and chronic lymphocytic leukaemia (CLL), are examples of contrasting B-cell cancers; BL is a highly aggressive lymphoid tumour, frequently affecting children, whilst CLL typically presents as an indolent, slow-progressing leukaemia affecting the elderly. The B-cell-specific over-expression of the myc and tcl1 oncogenes in mice induce spontaneous malignancies modelling BL and CLL, respectively. Quantitative mass spectrometry proteomics and isobaric labelling were employed to examine the biology underpinning contrasting Eμ-myc and Eμ-TCL1 B-cell tumours...
January 4, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28060806/high-throughput-sequencing-of-extracellular-rna-from-human-plasma
#9
Kirsty M Danielson, Renee Rubio, Fieda Abderazzaq, Saumya Das, Yaoyu E Wang
The presence and relative stability of extracellular RNAs (exRNAs) in biofluids has led to an emerging recognition of their promise as 'liquid biopsies' for diseases. Most prior studies on discovery of exRNAs as disease-specific biomarkers have focused on microRNAs (miRNAs) using technologies such as qRT-PCR and microarrays. The recent application of next-generation sequencing to discovery of exRNA biomarkers has revealed the presence of potential novel miRNAs as well as other RNA species such as tRNAs, snoRNAs, piRNAs and lncRNAs in biofluids...
2017: PloS One
https://www.readbyqxmd.com/read/28057705/translational-control-of-lipogenic-enzymes-in-the-cell-cycle-of-synchronous-growing-yeast-cells
#10
Heidi M Blank, Ricardo Perez, Chong He, Nairita Maitra, Richard Metz, Joshua Hill, Yuhong Lin, Charles D Johnson, Vytas A Bankaitis, Brian K Kennedy, Rodolfo Aramayo, Michael Polymenis
Translational control during cell division determines when cells start a new cell cycle, how fast they complete it, the number of successive divisions, and how cells coordinate proliferation with available nutrients. The translational efficiencies of mRNAs in cells progressing synchronously through the mitotic cell cycle, while preserving the coupling of cell division with cell growth, remain uninvestigated. We now report comprehensive ribosome profiling of a yeast cell size series from the time of cell birth, to identify mRNAs under periodic translational control...
January 5, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28056786/immune-adaptation-to-chronic-intense-exercise-training-new-microarray-evidence
#11
Dongmei Liu, Ru Wang, Ana R Grant, Jinming Zhang, Paul M Gordon, Yuqin Wei, Peijie Chen
BACKGROUND: Endurance exercise training, especially the high-intensity training, exhibits a strong influence on the immune system. However, the mechanisms underpinning the immune-regulatory effect of exercise remain unclear. Consequently, we chose to investigate the alterations in the transcriptional profile of blood leukocytes in young endurance athletes as compared with healthy sedentary controls, using Affymetrix human gene 1.1 ST array. RESULTS: Group differences in the transcriptome were analyzed using Intensity-based Hierarchical Bayes method followed by a Logistic Regression-based gene set enrichment method...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28053217/high-interlaboratory-reproducibility-and-accuracy-of-next-generation-sequencing-based-bacterial-genotyping-in-a-ring-trial
#12
Alexander Mellmann, Paal Skytt Andersen, Stefan Bletz, Alexander W Friedrich, Thomas A Kohl, Berit Lilje, Stefan Niemann, Karola Prior, John W Rossen, Dag Harmsen
Today, next-generation whole genome sequencing (WGS) technology is increasingly used to determine the genetic relationship of bacteria on a nearly whole genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring-trial comprising five laboratories to determine the reproducibility and accuracy of WGS-based typing.The participating laboratories sequenced 20 blind-coded Staphylococcus aureus DNA samples using the 250 bp paired-end chemistry for library preparation in a single sequencing run on an Illumina Miseq sequencer...
January 4, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28053107/domain-organization-and-evolution-of-the-highly-divergent-5-coding-region-of-genomes-of-arteriviruses-including-the-novel-possum-nidovirus
#13
Anastasia Gulyaeva, Magdalena Dunowska, Erik Hoogendoorn, Julia Giles, Dmitry Samborskiy, Alexander E Gorbalenya
: In five experimentally characterized arterivirus species, the 5' -end genome coding region comprises most divergent nonstructural proteins (nsp) 1 and 2 that include papain-like proteases (PLPs) and other poorly characterized domains. They are involved in regulation of transcription, polyprotein processing, and virus-host interaction. Here, we present results of bioinformatics analysis of this region of 14 arterivirus species, including that of the most distantly related wobbly possum disease virus (WPDV), determined by a modified 5' RACE protocol...
January 4, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28050984/evaluation-of-bacteriological-profile-in-the-apical-root-segment-of-the-patients-with-primary-apical-periodontitis
#14
Aravind Tatikonda, N Sudheep, Krishna P Biswas, K Gowtham, Sudarshan Pujari, Padam Singh
INTRODUCTION: Apical periodontitis usually results from bacterial accumulation and contamination occurring in the root-canal system, and extending beyond the apical foramen to involve the periapical tissues. Literature has a paucity of the studies that stress on the division and analysis of the pulp canal segments. The reason for this disparity might be the technique used for collecting the samples from the pulp canals. Hence, we carried out the present study to evaluate the microbial flora in the apical part of the roots with necrotic pulp canals...
January 1, 2017: Journal of Contemporary Dental Practice
https://www.readbyqxmd.com/read/28046103/transcriptome-profiling-identifies-ribosome-biogenesis-as-a-target-of-alcohol-teratogenicity-and-vulnerability-during-early-embryogenesis
#15
Mark E Berres, Ana Garic, George R Flentke, Susan M Smith
Fetal alcohol spectrum disorder (FASD) is a leading cause of neurodevelopmental disability. Individuals with FASD may exhibit a characteristic facial appearance that has diagnostic utility. The mechanism by which alcohol disrupts craniofacial development is incompletely understood, as are the genetic factors that can modify individual alcohol vulnerability. Using an established avian model, we characterized the cranial transcriptome in response to alcohol to inform the mechanism underlying these cells' vulnerability...
2017: PloS One
https://www.readbyqxmd.com/read/28046012/transcriptome-analysis-of-taxillusi-chinensis-dc-danser-seeds-in-response-to-water-loss
#16
Shugen Wei, Xiaojun Ma, Limei Pan, Jianhua Miao, Jine Fu, Longhua Bai, Zhonglian Zhang, Yanhong Guan, Changming Mo, Hao Huang, Maoshan Chen
BACKGROUND: Taxillus chinensis (DC.) Danser, the official species of parasitic loranthus that grows by parasitizing other plants, is used in various traditional Chinese medicine prescriptions. ABA-dependent and ABA-independent pathways are two major pathways in response to drought stress for plants and some genes have been reported to play a key role during the dehydration including dehydration-responsive protein RD22, late embryogenesis abundant (LEA) proteins, and various transcription factors (TFs) like MYB and WRKY...
2017: PloS One
https://www.readbyqxmd.com/read/28044276/antimicrobial-potential-and-taxonomic-investigation-of-piezotolerant-streptomyces-sp-niot-ch-40-isolated-from-deep-sea-sediment
#17
Vishnu Priya Padmanaban, Pankaj Verma, Srividhyalakshmi Venkatabaskaran, Thirupathi Keppayan, Dharani Gopal, Ashok Kumar Sekar, Kirubagaran Ramalingam
Microbial-derived natural products from extreme niches such as deepsea are known to possess structural and functional novelty. With this background, the present study was designed to investigate the bioprospecting potential and systematics of a deep-sea derived piezotolerant bacterial strain NIOT-Ch-40, showing affiliation to the genus Streptomyces based on 16S RNA gene similarity. Preliminary screening for the presence of biosynthetic genes like polyketide synthase I, polyketide synthase II, non ribosomal peptide synthase, 3-amino-5-hydroxybenzoic acid synthase and spiroindimicin followed by antibacterial activity testing confirmed the presence of potent bioactivity...
February 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28034797/expression-profile-of-rrbp1-genes-during-embryonic-development-and-in-adult-tissues-of-xenopus-laevis
#18
Guang-Hui Liu, Cheng-Zhou Mao, Hai-Yan Wu, Deng-Cheng Zhou, Jing-Bo Xia, Soo-Ki Kim, Dong-Qing Cai, Hui Zhao, Xu-Feng Qi
Recent studies suggest that ribosome-binding protein 1 (RRBP1) is involved in multiple diseases such as tumorigenesis and cardiomyopathies. However, its function during embryonic development remains largely unknown. We searched Xenopus laevis database with human RRBP1 protein sequence and identified two cDNA sequences encoding Xenopus orthologs of RRBP1 including rrbp1a (NM_001089623) and rrbp1b (NM_001092468). Both genes were firstly detected at blastula stage 8 with weak signals in animal hemisphere by whole mount in situ hybridization...
December 26, 2016: Gene Expression Patterns: GEP
https://www.readbyqxmd.com/read/28018335/metabolic-conservation-and-diversification-of-metarhizium-species-correlate-with-fungal-host-specificity
#19
Yong-Jiang Xu, Feifei Luo, Bing Li, Yanfang Shang, Chengshu Wang
The ascomycete genus Metarhizium contains several species of insect pathogenic fungi ranging from specialists with narrow host ranges to generalists that can infect diverse invertebrates. Genetic and metabolic conservations and diversifications of Metarhizium species are not well understood. In this study, using the genome information of seven Metarhizium species, we performed a comparative analysis of gene clusters involved in secondary metabolisms (SMs) in these species. The results revealed that the generalist species contain more SM gene clusters than the specialists, and that both conserved and divergent evolutions may have occurred in SM genes during fungal speciation...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28005933/differential-regulation-of-rrna-and-trna-transcription-from-the-rrna-trna-composite-operon-in-escherichia-coli
#20
Hiraku Takada, Tomohiro Shimada, Debashish Dey, M Zuhaib Quyyum, Masahiro Nakano, Akira Ishiguro, Hideji Yoshida, Kaneyoshi Yamamoto, Ranjan Sen, Akira Ishihama
Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order) and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP) holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons...
2016: PloS One
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