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https://www.readbyqxmd.com/read/28100609/sterol-binding-by-the-tombusviral-replication-proteins-is-essential-for-replication-in-yeast-and-plants
#1
Kai Xu, Peter D Nagy
: Membranous structures derived from various organelles are important for replication of plus-stranded RNA viruses. Although the important roles of co-opted host proteins in RNA virus replication have been appreciated for a decade, the equally important functions of cellular lipids in virus replication are gaining full attention only recently. Previous works with Tomato bushy stunt tombusvirus (TBSV) in model host yeast have revealed essential roles for phosphatidylethanolamine and sterols in viral replication...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28096443/stem-loop-rna-labeling-can-affect-nuclear-and-cytoplasmic-mrna-processing
#2
Stephanie Heinrich, Corinne L Sidler, Claus M Azzalin, Karsten Weis
The binding of sequence-specific RNA-interacting proteins, such as the bacteriophage MS2 or PP7 coat proteins, to their corresponding target sequences has been extremely useful and widely used to visualize single mRNAs in vivo. However, introduction of MS2 stem-loops into yeast mRNAs has recently been shown to lead to the accumulation of RNA fragments, suggesting that the loops impair mRNA decay. This result was questioned, because fragment occurrence was mainly assessed using ensemble methods, and their cellular localization and its implications had not been addressed on a single transcript level...
February 2017: RNA
https://www.readbyqxmd.com/read/28095716/circrnas-a-regulator-of-cellular-stress
#3
Joseph W Fischer, Anthony K L Leung
Circular RNAs (CircRNAs) were first identified as a viroid and later found to also be an endogenous RNA splicing product in eukaryotes. In recent years, a series of RNA-sequencing analyses from a diverse range of eukaryotes have shed new light on these eukaryotic circRNAs, revealing dynamic expression patterns in various developmental stages and physiological conditions. In this review, we focus on circRNAs implicated in stress response pathways and explore potential mechanisms underlying their regulation. To date, circRNAs have been shown to act as scaffolds in the assembly of protein complexes, sequester proteins from native subcellular localization, activate transcription of parental genes, inhibit RNA-protein interactions, and function as regulators of microRNA activity...
January 17, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28088779/comprehensive-proteome-analysis-of-lysosomes-reveals-the-diverse-function-of-macrophages-in-immune-responses
#4
Yanpan Gao, Yanyu Chen, Shaohua Zhan, Wenhao Zhang, Feng Xiong, Wei Ge
Phagocytosis and autophagy in macrophages have been shown to be essential to both innate and adaptive immunity. Lysosomes are the main catabolic subcellular organelles responsible for degradation and recycling of both extracellular and intracellular material, which are the final steps in phagocytosis and autophagy. However, the molecular mechanisms underlying lysosomal functions after infection remain obscure. In this study, we conducted a quantitative proteomics analysis of the changes in constitution and glycosylation of proteins in lysosomes derived from murine RAW 264...
January 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28078793/insights-into-nuclear-dynamics-using-live-cell-imaging-approaches
#5
REVIEW
Rachel B Bigley, Alexander Y Payumo, Jeffrey M Alexander, Guo N Huang
The nucleus contains the genetic blueprint of the cell and myriad interactions within this subcellular structure are required for gene regulation. In the current scientific era, characterization of these gene regulatory networks through biochemical techniques coupled with systems-wide 'omic' approaches has become commonplace. However, these strategies are limited because they represent a mere snapshot of the cellular state. To obtain a holistic understanding of nuclear dynamics, relevant molecules must be studied in their native contexts in living systems...
January 12, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28053097/subcellular-localization-of-hiv-1-gag-pol-mrnas-regulates-sites-of-virion-assembly
#6
Jordan T Becker, Nathan M Sherer
: HIV-1 full-length, unspliced RNAs serve dual roles in the cytoplasm as mRNAs encoding the Gag and Gag-Pol capsid proteins as well as genomic RNAs (gRNAs) packaged by Gag into virions undergoing assembly at the plasma membrane (PM). Because Gag is sufficient to drive assembly of virus-like particles even in the absence of gRNA binding, whether viral RNA trafficking plays an active role in the native assembly pathway is unknown. In this study we tested the effects of modulating the cytoplasmic abundance or distribution of full-length viral RNAs on Gag trafficking and assembly in the context of single cells...
January 4, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28031329/hur-enhances-early-restitution-of-the-intestinal-epithelium-by-increasing-cdc42-translation
#7
Lan Liu, Ran Zhuang, Lan Xiao, Hee Kyoung Chung, Jason Luo, Douglas J Turner, Jaladanki N Rao, Myriam Gorospe, Jian-Ying Wang
The mammalian intestinal mucosa exhibits a spectrum of responses after acute injury and repairs itself rapidly to restore the epithelial integrity. The RNA-binding protein HuR regulates the stability and translation of target mRNAs and is involved in many aspects of gut epithelium homeostasis, but its exact role in the regulation of mucosal repair after injury remains unknown. Here we show that HuR is essential for early intestinal epithelial restitution by increasing the expression of cell division control protein 42 (Cdc42) at the posttranscriptional level...
December 28, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28018416/functional-and-rna-sequencing-analysis-revealed-expression-of-a-novel-stay-green-gene-from-zoysia-japonica-zjsgr-caused-chlorophyll-degradation-and-accelerated-senescence-in-arabidopsis
#8
Ke Teng, Zhihui Chang, Xiao Li, Xinbo Sun, Xiaohong Liang, Lixin Xu, Yuehui Chao, Liebao Han
Senescence is not only an important developmental process, but also a responsive regulation to abiotic and biotic stress for plants. Stay-green protein plays crucial roles in plant senescence and chlorophyll degradation. However, the underlying mechanisms were not well-studied, particularly in non-model plants. In this study, a novel stay-green gene, ZjSGR, was isolated from Zoysia japonica. Subcellular localization result demonstrated that ZjSGR was localized in the chloroplasts. Quantitative real-time PCR results together with promoter activity determination using transgenic Arabidopsis confirmed that ZjSGR could be induced by darkness, ABA and MeJA...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28017373/mutations-in-ebf3-disturb-transcriptional-profiles-and-cause-intellectual-disability-ataxia-and-facial-dysmorphism
#9
Frederike Leonie Harms, Katta M Girisha, Andrew A Hardigan, Fanny Kortüm, Anju Shukla, Malik Alawi, Ashwin Dalal, Lauren Brady, Mark Tarnopolsky, Lynne M Bird, Sophia Ceulemans, Martina Bebin, Kevin M Bowling, Susan M Hiatt, Edward J Lose, Michelle Primiano, Wendy K Chung, Jane Juusola, Zeynep C Akdemir, Matthew Bainbridge, Wu-Lin Charng, Margaret Drummond-Borg, Mohammad K Eldomery, Ayman W El-Hattab, Mohammed A M Saleh, Stéphane Bézieau, Benjamin Cogné, Bertrand Isidor, Sébastien Küry, James R Lupski, Richard M Myers, Gregory M Cooper, Kerstin Kutsche
From a GeneMatcher-enabled international collaboration, we identified ten individuals affected by intellectual disability, speech delay, ataxia, and facial dysmorphism and carrying a deleterious EBF3 variant detected by whole-exome sequencing. One 9-bp duplication and one splice-site, five missense, and two nonsense variants in EBF3 were found; the mutations occurred de novo in eight individuals, and the missense variant c.625C>T (p.Arg209Trp) was inherited by two affected siblings from their healthy mother, who is mosaic...
January 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27999994/functional-characterisation-of-the-yipf-protein-family-in-mammalian-cells
#10
Tilen Kranjc, Eugene Dempsey, Gerard Cagney, Nobuhiro Nakamura, Denis C Shields, Jeremy C Simpson
In this study, we carry out a systematic characterisation of the YIPF family of proteins with respect to their subcellular localisation profile, membrane topology and functional effects on the endomembrane system. YIPF proteins primarily localise to the Golgi complex and can be grouped into trans-Golgi-localising YIPFs (YIPF1 and YIPF2) and cis-Golgi-localising YIPFs (YIPF3, YIPF4 and YIPF5), with YIPF6 and YIPF7 showing a broader profile being distributed throughout the Golgi stack. YIPF proteins have a long soluble N-terminal region, which is orientated towards the cytosol, followed by 5 closely stacked transmembrane domains, and a C terminus, orientated towards the lumen of the Golgi...
December 20, 2016: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/27975273/localization-in-oogenesis-of-maternal-regulators-of-embryonic-development
#11
Matias Escobar-Aguirre, Yaniv M Elkouby, Mary C Mullins
Cell polarity generates intracellular asymmetries and functional regionalization in tissues and morphogenetic processes. Cell polarity in development often relies on mechanisms of RNA localization to specific subcellular domains to define the identity of future developing tissues. The totipotent egg of most animals illustrates in a grand way the importance of cell polarity and RNA localization in regulating multiple crucial developmental events. The polarization of the egg arises during its development in oogenesis...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27959965/functional-analyses-of-the-crohn-s-disease-risk-gene-lacc1
#12
Ghazaleh Assadi, Liselotte Vesterlund, Ferdinando Bonfiglio, Luca Mazzurana, Lina Cordeddu, Danika Schepis, Jenny Mjösberg, Sabrina Ruhrmann, Alessia Fabbri, Vladana Vukojevic, Piergiorgio Percipalle, Florian A Salomons, Jurga Laurencikiene, Leif Törkvist, Jonas Halfvarson, Mauro D'Amato
BACKGROUND: Genetic variation in the Laccase (multicopper oxidoreductase) domain-containing 1 (LACC1) gene has been shown to affect the risk of Crohn's disease, leprosy and, more recently, ulcerative colitis and juvenile idiopathic arthritis. LACC1 function appears to promote fatty-acid oxidation, with concomitant inflammasome activation, reactive oxygen species production, and anti-bacterial responses in macrophages. We sought to contribute to elucidating LACC1 biological function by extensive characterization of its expression in human tissues and cells, and through preliminary analyses of the regulatory mechanisms driving such expression...
2016: PloS One
https://www.readbyqxmd.com/read/27956705/arfgap-domain-containing-protein-2-adap2-integrates-upstream-and-downstream-modules-of-rig-i-signaling-and-facilitates-type-i-interferon-production
#13
Pradeep Bist, Soo Yeon Kim, Niyas Kudukil Pulloor, Kathleen McCaffrey, Sajith Kumar Nair, Yiliu Liu, Rongtuan Lin, Manoj N Krishnan
: Transcription of Type I interferon during RNA virus infection requires signal communication between several Pattern recognition receptor (PRR)-adaptor complexes located at distinct subcellular membranous compartments and a central cytoplasmic TBK1-IRF3 kinase-transcription factor module. However, how cell integrates signal transduction through spatially distinct modules of antiviral signaling pathways is less defined. RIG-I is a major cytosolic PRR involved in the control of several RNA viruses...
December 12, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27956586/dna-methylation-influences-the-expression-of-dicer-like4-isoforms-which-encode-proteins-of-alternative-localization-and-function
#14
Nathan Pumplin, Alexis Sarazin, Pauline E Jullien, Nicolas G Bologna, Stefan Oberlin, Olivier Voinnet
Plant RNA silencing operates via RNA-directed DNA-methylation (RdDM) to repress transcription or by targeting mRNAs via posttranscriptional gene silencing (PTGS). These pathways rely on distinct Dicer-like (DCL) proteins that process double-stranded RNA (dsRNA) into small-interfering RNAs (siRNAs). Here, we explored the expression and subcellular localization of Arabidopsis thaliana DCL4. DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic protein, which also represents the ancestral form in plants...
November 2016: Plant Cell
https://www.readbyqxmd.com/read/27941027/the-lipid-droplet-associated-protein-perilipin-3-facilitates-hepatitis-c-virus-driven-hepatic-steatosis
#15
Daniel Ferguson, Jun Zhang, Matthew A Davis, Robert N Helsley, Lise-Lotte Vedin, Richard G Lee, Rosanne M Crooke, Mark J Graham, Paolo Parini, J Mark Brown
Hepatitis C Virus (HCV) is an enveloped RNA virus responsible for 170 million cases of viral hepatitis worldwide. Over 50% of chronically infected HCV patients develop hepatic steatosis, and steatosis can be induced by expression of HCV core protein (core) alone. Additionally, core must associate with cytoplasmic lipid droplets (LD) for steatosis development and viral particle assembly. Given the LD is an important component of hepatic lipid storage, and serves as a platform for HCV particle assembly; this dynamic subcellular organelle is a gatekeeper in the pathogenesis of viral hepatitis...
December 10, 2016: Journal of Lipid Research
https://www.readbyqxmd.com/read/27932311/daclatasvir-prevents-hepatitis-c-virus-by-blocking-transfer-of-viral-genome-to-assembly-sites
#16
Bertrand Boson, Solène Denolly, Fanny Turlure, Christophe Chamot, Marlène Dreux, François-Loïc Cosset
BACKGROUND & AIMS: Daclatasvir is a direct-acting antiviral agent and potent inhibitor of NS5A, which is involved in replication of the hepatitis C virus (HCV) genome, presumably via membranous web shaping, and assembly of new virions, likely via transfer of the HCV RNA genome to viral particle assembly sites. Daclatasvir inhibits the formation of new membranous web structures and, ultimately, of replication complex vesicles, but also inhibits an early assembly step. We investigated the relationship between daclatasvir-induced clustering of HCV proteins, intracellular localization of viral RNAs and inhibition of viral particle assembly...
December 5, 2016: Gastroenterology
https://www.readbyqxmd.com/read/27928005/amino-acid-mutations-in-the-ns4a-region-of-hepatitis-c-virus-contribute-to-viral-replication-and-infectious-virus-production
#17
Asako Murayama, Nao Sugiyama, Ryosuke Suzuki, Masaki Moriyama, Noriko Nakamura, Hidenori Mochizuki, Takaji Wakita, Takanobu Kato
: Hepatitis C Virus (HCV) strain JFH-1, which belongs to genotype 2a, replicates autonomously in cultured cells, whereas another genotype 2a strain, J6CF, does not. Previously, we found that replacing the NS3 helicase and NS5B-to-3' X regions of J6CF with those of JFH-1 confers J6CF replication competence. In this study, we aimed to identify the minimum modifications to establish replication-competent J6CF within these genomic regions. We previously identified 4 mutations in the NS5B-to-3' X region that confer J6CF replication competence instead of replacing of this region...
December 7, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27922192/evidence-for-pipecolate-oxidase-in-mediating-protection-against-hydrogen-peroxide-stress
#18
Sathish Kumar Natarajan, Ezhumalai Muthukrishnan, Oleh Khalimonchuk, Justin L Mott, Donald F Becker
Pipecolate, an intermediate of the lysine catabolic pathway, is oxidized to Δ(1) -piperideine-6-carboxylate (P6C) by the flavoenzyme l-pipecolate oxidase (PIPOX). P6C spontaneously hydrolyzes to generate α-aminoadipate semialdehyde, which is then converted into α-aminoadipate acid by α-aminoadipatesemialdehyde dehydrogenase. l-pipecolate was previously reported to protect mammalian cells against oxidative stress. Here, we examined whether PIPOX is involved in the mechanism of pipecolate stress protection...
December 6, 2016: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/27921095/journey-from-the-center-of-the-cell-the-intra-and-intercellular-transport-of-mrna
#19
REVIEW
Anna Kasprowicz-Maluśki, Wojciech Kwiatkowski, Alicja Starosta, Przemysław Wojtaszek
Transport and localized translation of mRNA is crucial for the proper spatiotemporal organization of proteins within cells. Distribution of RNAs to subcellular domains has recently emerged as a major mechanism for establishing functionally distinct compartments and structures in the cells. There is an emerging evidence that active transport of mRNA involves cytoskeleton and membrane trafficking pathways in fungi, plants and animals, suggesting that it is a common phenomenon among eukaryotes. The important highlights are that the RNA-binding proteins recognize the cargo mRNA and that RNPs are actively transported on the cytoskeletal tracks or co-transported with membranous compartments, such as the endoplasmic reticulum and endosomes...
2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27920150/heterotrimeric-kinesin-2-together-with-kinesin-1-steers-vesicular-acetylcholinesterase-movements-toward-the-synapse
#20
Anuttama Kulkarni, Yasmin Khan, Krishanu Ray
Acetylcholinesterase (AChE), which is implicated in the pathophysiology of neurological disorders, is distributed along the axon and enriched at the presynaptic basal lamina. It hydrolyses the neurotransmitter acetylcholine, which inhibits synaptic transmission. Aberrant AChE activity and ectopic axonal accumulation of the enzyme are associated with neurodegenerative disorders, such as Alzheimer's disease. The molecular mechanism that underlies AChE transport is still unclear. Here, we show that expression of Drosophila AChE tagged with photoactivable green fluorescent protein and m-Cherry (GPAC) in cholinergic neurons compensates for the RNA interference-mediated knockdown of endogenous AChE activity...
December 5, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
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