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https://www.readbyqxmd.com/read/28216671/dual-mechanisms-regulate-the-nucleocytoplasmic-localization-of-human-ddx6
#1
Jo-Hsi Huang, Wei-Chi Ku, Yen-Chun Chen, Yi-Ling Chang, Chia-Ying Chu
DDX6 is a conserved DEAD-box protein (DBP) that plays central roles in cytoplasmic RNA regulation, including processing body (P-body) assembly, mRNA decapping, and translational repression. Beyond its cytoplasmic functions, DDX6 may also have nuclear functions because its orthologues are known to localize to nuclei in several biological contexts. However, it is unclear whether DDX6 is generally present in human cell nuclei, and the molecular mechanism underlying DDX6 subcellular distribution remains elusive...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28212430/a-calmodulin-like-protein-suppresses-rna-silencing-and-promotes-geminivirus-infection-by-degrading-sgs3-via-the-autophagy-pathway-in-nicotiana-benthamiana
#2
Fangfang Li, Nan Zhao, Zhenghe Li, Xiongbiao Xu, Yaqin Wang, Xiuling Yang, Shu-Sheng Liu, Aiming Wang, Xueping Zhou
A recently characterized calmodulin-like protein is an endogenous RNA silencing suppressor that suppresses sense-RNA induced post-transcriptional gene silencing (S-PTGS) and enhances virus infection, but the mechanism underlying calmodulin-like protein-mediated S-PTGS suppression is obscure. Here, we show that a calmodulin-like protein from Nicotiana benthamiana (NbCaM) interacts with Suppressor of Gene Silencing 3 (NbSGS3). Deletion analyses showed that domains essential for the interaction between NbSGS3 and NbCaM are also required for the subcellular localization of NbSGS3 and NbCaM suppressor activity...
February 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28212420/transcriptome-using-illumina-sequencing-reveals-the-traits-of-spermatogenesis-and-developing-testes-in-eriocheir-sinensis
#3
Gen-Liang Li, Hui Qian
Chinese mitten crab (Eriocheir sinensis) has the spermatozoa with typical aflagellate, decondensed chromatin, cup-shaped nuclei, and radial arms. However, the mechanism of spermatogenesis during which the specific spermatozoa are generated in this species is yet unclear. Here, the transcriptome of developing testis in E. sinensis was analyzed using the ways of RNA-seq and bioinformatics analysis to identify candidate genes potentially involved in development of testis and spermatogenesis. The Illumina HiSeq2500 sequencing of three replicons of samples produced a total of 145...
2017: PloS One
https://www.readbyqxmd.com/read/28202040/subcellular-localization-and-interactions-of-infectious-salmon-anemia-virus-isav-m1-and-nep-as-well-as-host-hsc70
#4
Wenting Zhang, Chengzhi Cai, Li Lin, Yizhi Jane Tao, Meilin Jin
BACKGROUND: Infectious salmon anemia virus (ISAV) is an important fish pathogen that causes high mortality in farmed Atlantic salmon. The ISAV genome consists of eight single-stranded, negative-sense RNA segments. The six largest segments contain one open reading frame (ORF) each, and encode three polymerase proteins, nucleoprotein, fusion protein, and hemagglutinin esterase protein. The two smallest segments contain more than one ORF each. The segment 7 encodes non-structural protein 1 (NS1) and nuclear export protein (NEP), while segment 8 encodes matrix protein 1 and 2 (M1 and M2)...
February 15, 2017: Virology Journal
https://www.readbyqxmd.com/read/28199211/endocytosis-and-membrane-receptor-internalization-implication-of-f-bar-protein-carom
#5
Yanjie Xu, Jixiang Xia, Suxuan Liu, Sam Stein, Cueto Ramon, Hang Xi, Luqiao Wang, Xinyu Xiong, Lixiao Zhang, Dingwen He, William Yang, Xianxian Zhao, Xiaoshu Cheng, Xiaofeng Yang, Hong Wang
Endocytosis is a cellular process mostly responsible for membrane receptor internalization. Cell membrane receptors bind to their ligands and form a complex which can be internalized. We previously proposed that F-BAR protein initiates membrane curvature and mediates endocytosis via its binding partners. However, F-BAR protein partners involved in membrane receptor endocytosis and the regulatory mechanism remain unknown. In this study, we established database mining strategies to explore mechanisms underlying receptor-related endocytosis...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28199000/overexpression-of-pregnane-x-and-glucocorticoid-receptors-and-the-regulation-of-cytochrome-p450-in-human-epileptic-brain-endothelial-cells
#6
Chaitali Ghosh, Mohammed Hossain, Jesal Solanki, Imad M Najm, Nicola Marchi, Damir Janigro
OBJECTIVE: Recent evidence suggests a metabolic contribution of cytochrome P450 enzymes (CYPs) to the drug-resistant phenotype in human epilepsy. However, the upstream molecular regulators of CYP in the epileptic brain remain understudied. We therefore investigated the expression and function of pregnane xenobiotic (PXR) and glucocorticoid (GR) nuclear receptors in endothelial cells established from post-epilepsy surgery brain samples. METHODS: PXR/GR localization was evaluated by immunohistochemistry in specimens from subjects who underwent temporal lobe resections to relieve drug-resistant seizures...
February 15, 2017: Epilepsia
https://www.readbyqxmd.com/read/28188285/rna-binding-protein-quaking-stabilizes-sirt2-mrna-during-oligodendroglial-differentiation
#7
Merlin P Thangaraj, Kendra L Furber, Jotham K Gan, Shaoping Ji, Larhonda Sobchishin, J Ronald Doucette, Adil J Nazarali
Myelination is controlled by timely expression of genes involved in the differentiation of oligodendrocyte precursor cells (OPCs) into myelinating oligodendrocytes (OLs). Sirtuin 2 (SIRT2), a NAD+-dependent deacetylase, plays a critical role in OL differentiation by promoting both arborization and downstream expression of myelin specific genes. However, the mechanisms involved in regulating SIRT2 expression during OL development are largely unknown. The RNA binding protein Quaking (QKI) plays an important role in myelination by post-transcriptionally regulating the expression of several myelin specific genes...
February 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28179879/cannabinoid-receptors-modulate-neuronal-morphology-and-ankyring-density-at-the-axon-initial-segment
#8
Mónica Tapia, Ana Dominguez, Wei Zhang, Ana Del Puerto, María Ciorraga, María José Benitez, Carmen Guaza, Juan José Garrido
Neuronal polarization underlies the ability of neurons to integrate and transmit information. This process begins early in development with axon outgrowth, followed by dendritic growth and subsequent maturation. In between these two steps, the axon initial segment (AIS), a subcellular domain crucial for generating action potentials (APs) and maintaining the morphological and functional polarization, starts to develop. However, the cellular/molecular mechanisms and receptors involved in AIS initial development and maturation are mostly unknown...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28179528/identification-of-novel-functions-for-hepatitis-c-virus-envelope-glycoprotein-e1-in-virus-entry-and-assembly
#9
Juliano Haddad, Yves Rouillé, Xavier Hanoulle, Véronique Descamps, Monzer Hamze, Fouad Dabboussi, Thomas F Baumert, Gilles Duverlie, Muriel Lavie, Jean Dubuisson
Hepatitis C Virus (HCV) envelope glycoprotein complex is composed of E1 and E2 subunits. E2 is the receptor-binding protein as well as the major target of neutralizing antibodies, whereas the functions of E1 remain poorly defined. Here, we took advantage of the recently published structure of the N-terminal region of E1 ectodomain to interrogate the functions of this glycoprotein by mutating residues within this 79 amino acid region in the context of an infectious clone. The phenotypes of the mutants were characterized to determine the effects of the mutations on virus entry, replication and assembly...
February 8, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28177844/genome-wide-analysis-and-expression-characteristics-of-small-auxin-up-rna-saur-genes-in-moso-bamboo-phyllostachys-edulis
#10
Qingsong Bai, Dan Hou, Long Li, Zhanchao Cheng, Wei Ge, Jun Liu, Xueping Li, Shaohua Mu, Jian Gao
Moso bamboo (Phyllostachys edulis) is well-known for its rapid shoot growth. Auxin exerts pleiotropic effects on plant growth. The small auxin-up RNA (SAUR) genes are early auxin-responsive genes involved in plant growth. In total, 38 SAUR genes were identified in P. edulis (PheSAUR). A comprehensive overview of the PheSAUR gene family is presented, including the gene structures, phylogeny and subcellular location predictions. A transcriptome analysis indicated that 37 (except PheSAUR18) of the PheSAUR genes were expressed during shoot growth process and the PheSAUR genes were differentially expressed...
November 15, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28163695/acth-action-on-messenger-rna-stability-mechanisms
#11
Agnès Desroches-Castan, Jean-Jacques Feige, Nadia Cherradi
The regulation of mRNA stability has emerged as a critical control step in dynamic gene expression. This process occurs in response to modifications of the cellular environment, including hormonal variations, and regulates the expression of subsets of proteins whose levels need to be rapidly adjusted. Modulation of messenger RNA stability is usually mediated by stabilizing or destabilizing RNA-binding proteins (RNA-BP) that bind to the 3'-untranslated region regulatory motifs, such as AU-rich elements (AREs)...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/28155669/genome-wide-analysis-of-mrnas-associated-with-mouse-peroxisomes
#12
Aliaksandr A Yarmishyn, Maksym Kremenskoy, Arsen O Batagov, Axel Preuss, Jin Huei Wong, Igor V Kurochkin
BACKGROUND: RNA is often targeted to be localized to the specific subcellular compartments. Specific localization of mRNA is believed to be an important mechanism for targeting their protein products to the locations, where their function is required. RESULTS: In this study we performed the genome wide transcriptome analysis of peroxisome preparations from the mouse liver using microarrays. We demonstrate that RNA is absent inside peroxisomes, however it is associated at their exterior via the noncovalent contacts with the membrane proteins...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28154139/harnessing-host-ros-generating-machinery-for-the-robust-genome-replication-of-a-plant-rna-virus
#13
Kiwamu Hyodo, Kenji Hashimoto, Kazuyuki Kuchitsu, Nobuhiro Suzuki, Tetsuro Okuno
As sessile organisms, plants have to accommodate to rapid changes in their surrounding environment. Reactive oxygen species (ROS) act as signaling molecules to transduce biotic and abiotic stimuli into plant stress adaptations. It is established that a respiratory burst oxidase homolog B of Nicotiana benthamiana (NbRBOHB) produces ROS in response to microbe-associated molecular patterns to inhibit pathogen infection. Plant viruses are also known as causative agents of ROS induction in infected plants; however, the function of ROS in plant-virus interactions remains obscure...
February 1, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28134780/viral-vector-mediated-antisense-therapy-for-genetic-diseases
#14
REVIEW
Marine Imbert, Gabriella Dias-Florencio, Aurélie Goyenvalle
RNA plays complex roles in normal health and disease and is becoming an important target for therapeutic intervention; accordingly, therapeutic strategies that modulate RNA function have gained great interest over the past decade. Antisense oligonucleotides (AOs) are perhaps the most promising strategy to modulate RNA expression through a variety of post binding events such as gene silencing through degradative or non-degradative mechanisms, or splicing modulation which has recently demonstrated promising results...
January 26, 2017: Genes
https://www.readbyqxmd.com/read/28132027/drnapred-fast-sequence-based-method-that-accurately-predicts-and-discriminates-dna-and-rna-binding-residues
#15
Jing Yan, Lukasz Kurgan
Protein-DNA and protein-RNA interactions are part of many diverse and essential cellular functions and yet most of them remain to be discovered and characterized. Recent research shows that sequence-based predictors of DNA-binding residues accurately find these residues but also cross-predict many RNA-binding residues as DNA-binding, and vice versa. Most of these methods are also relatively slow, prohibiting applications on the whole-genome scale. We describe a novel sequence-based method, DRNApred, which accurately and in high-throughput predicts and discriminates between DNA- and RNA-binding residues...
January 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28123063/lipid-flippases-promote-antiviral-silencing-and-the-biogenesis-of-viral-and-host-sirnas-in-arabidopsis
#16
Zhongxin Guo, Jinfeng Lu, Xianbing Wang, Binhui Zhan, Wanxiang Li, Shou-Wei Ding
Dicer-mediated processing of virus-specific dsRNA into short interfering RNAs (siRNAs) in plants and animals initiates a specific antiviral defense by RNA interference (RNAi). In this study, we developed a forward genetic screen for the identification of host factors required for antiviral RNAi in Arabidopsis thaliana Using whole-genome sequencing and a computational pipeline, we identified aminophospholipid transporting ATPase 2 (ALA2) and the related ALA1 in the type IV subfamily of P-type ATPases as key components of antiviral RNAi...
February 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28112241/transit-peptide-elements-mediate-selective-protein-targeting-to-two-different-types-of-chloroplasts-in-the-single-cell-c4-species-bienertia-sinuspersici
#17
Diana Wimmer, Philipp Bohnhorst, Vinay Shekhar, Inhwan Hwang, Sascha Offermann
Bienertia sinuspersici is a terrestrial plant that performs C4 photosynthesis within individual cells through operating a carbon concentrating mechanism between different subcellular domains including two types of chloroplasts. It is currently unknown how differentiation of two highly specialized chloroplasts within the same cell occurs as no similar cases have been reported. Here we show that this differentiation in photosynthetic cells of B. sinuspersici is enabled by a transit peptide (TP) mediated selective protein targeting mechanism...
January 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28100609/sterol-binding-by-the-tombusviral-replication-proteins-is-essential-for-replication-in-yeast-and-plants
#18
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
#19
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
#20
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
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