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Spliceosome

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https://www.readbyqxmd.com/read/29228330/spliceosomal-protein-u1a-is-involved-in-alternative-splicing-and-salt-stress-tolerance-in-arabidopsis-thaliana
#1
Jinbao Gu, Zhiqiang Xia, Yuehua Luo, Xingyu Jiang, Bilian Qian, He Xie, Jian-Kang Zhu, Liming Xiong, Jianhua Zhu, Zhen-Yu Wang
Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spliceosome-mediated alternative splicing (AS) is essential in these adaptive processes. However, the functions of the spliceosome in plant stress responses are poorly understood. Here, we report the in-depth characterization of a U1 spliceosomal protein, AtU1A, in controlling AS of pre-mRNAs under salt stress and salt stress tolerance in Arabidopsis thaliana...
December 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29228309/prp8-intein-in-dermatophytes-evolution-and-species-identification
#2
Hans Garcia Garces, Raquel Theodoro Cordeiro, E Bagagli
Dermatophytes are keratinophilic fungi belonging to the family Arthrodermataceae. Despite having a monophyletic origin, its systematics has always been complex and controversial. Sequencing of nuclear ribosomal ITS and D1/D2 rDNA has been proposed as an efficient tool for identifying species in this group of fungi, while multilocus analyses have been used for phylogenetic species recognition. However, the search for new markers, with sequence and size variation, which enable species identification in only one polymerase chain reaction (PCR) step, is very attractive...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29222335/single-cell-transcriptome-sequencing-reveals-that-cell-division-cycle-5-like-protein-is-essential-for-porcine-oocyte-maturation
#3
Xiao-Man Liu, Yan-Kui Wang, Yun-Hua Liu, Xiao-Xia Yu, Pei-Chao Wang, Xuan Li, Zhi-Qiang Du, Cai-Xia Yang
The brilliant cresyl blue (BCB) test is used in both basic biological research and assisted reproduction to identify oocytes likely to be developmentally competent. However, the underlying molecular mechanism targeted by the BCB test is still unclear. To explore this question, we first confirmed that BCB-positive porcine oocytes had higher rates of meiotic maturation, better rates of cleavage and development into blastocysts, and lower death rates. Subsequent single-cell transcriptome sequencing on porcine germinal vesicle (GV)-stage oocytes identified 155 genes that were significantly differentially expressed between BCB-negative and BCB-positive oocytes...
December 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29221110/a-seven-gene-signature-predicts-overall-survival-of-patients-with-colorectal-cancer
#4
Huarong Chen, Xiaoqiang Sun, Weiting Ge, Yun Qian, Rui Bai, Shu Zheng
Colorectal cancer (CRC) is a major cause of global cancer mortality. Gene expression profiles can help predict prognosis of patients with CRC. In most of previous studies, disease recurrence was analyzed as the survival endpoint. Thus we aim to build a robust gene signature for prediction of overall survival (OS) in patients with CRC. Fresh frozen CRC tissues from 64 patients were analyzed using Affymetrix HG-U133plus 2.0 gene arrays. By performing univariate survival analysis, 6487 genes were found to be associated with the OS in our cohort...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29212152/prpf8-is-important-for-brca1-mediated-homologous-recombination
#5
David O Onyango, Gabriella Lee, Jeremy M Stark
Disruption of RNA splicing causes genome instability, which could contribute to cancer etiology. Furthermore, RNA splicing is an emerging anti-cancer target. Thus, we have evaluated the influence of the spliceosome factor PRPF8 and the splicing inhibitor Pladienolide B (PlaB) on homologous recombination (HR). We find that PRPF8 depletion and PlaB treatment cause a specific defect in homology-directed repair (HDR), and single strand annealing (SSA), which share end resection as a common intermediate, and BRCA1 as a required factor...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29191215/domestication-of-self-splicing-introns-during-eukaryogenesis-the-rise-of-the-complex-spliceosomal-machinery
#6
REVIEW
Julian Vosseberg, Berend Snel
ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated...
December 1, 2017: Biology Direct
https://www.readbyqxmd.com/read/29174924/the-output-of-protein-coding-genes-shifts-to-circular-rnas-when-the-pre-mrna-processing-machinery-is-limiting
#7
Dongming Liang, Deirdre C Tatomer, Zheng Luo, Huang Wu, Li Yang, Ling-Ling Chen, Sara Cherry, Jeremy E Wilusz
Many eukaryotic genes generate linear mRNAs and circular RNAs, but it is largely unknown how the ratio of linear to circular RNA is controlled or modulated. Using RNAi screening in Drosophila cells, we identify many core spliceosome and transcription termination factors that control the RNA outputs of reporter and endogenous genes. When spliceosome components were depleted or inhibited pharmacologically, the steady-state levels of circular RNAs increased while expression of their associated linear mRNAs concomitantly decreased...
November 9, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29168419/truncated-forms-of-u2-snrna-u2-tfs-are-shunted-toward-a-novel-uridylylation-pathway-that-differs-from-the-degradation-pathway-for-u1-tfs
#8
Hideaki Ishikawa, Yuko Nobe, Keiichi Izumikawa, Masato Taoka, Yoshio Yamauchi, Hiroshi Nakayama, Richard J Simpson, Toshiaki Isobe, Nobuhiro Takahash
During the biogenesis of U1 small nuclear ribonucleoprotein, a small population of U1 snRNA molecules receives an extra methylation at the first transcribed nucleotide and nucleolytic cleavage to remove the 3' structured region including the Sm protein-binding site and stem-loop 4. These modifications occur before hypermethylation of the monomethylated 5' cap, and produce truncated forms of U1 snRNA (U1-tfs) that are diverted from the normal pathway to a processing body-associated degradation pathway. Here, we demonstrate that a small population of U2 snRNA molecules receives post-transcriptional modifications similar to those of U1 to yield U2-tfs...
November 23, 2017: RNA Biology
https://www.readbyqxmd.com/read/29165698/nuclear-mrna-degradation-tunes-the-gain-of-the-unfolded-protein-response-in-saccharomyces-cerevisiae
#9
Debasish Sarkar, Sunirmal Paira, Biswadip Das
Unfolded protein response (UPR) is triggered by the accumulation of unfolded proteins in the endoplasmic reticulum (ER), which is accomplished by a dramatic induction of genes encoding ER chaperones. Activation of these genes involves their rapid transcription by Hac1p, encoded by the HAC1 precursor transcript harboring an intron and a bipartite element (3'-BE) in the 3'-UTR. ER stress facilitates intracellular targeting and recruitment of HAC1 pre-mRNA to Ire1p foci (requiring 3'-BE), leading to its non-spliceosomal splicing mediated by Ire1p/Rlg1p...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29162741/nuclear-hyaluronidase-2-drives-alternative-splicing-of-cd44-pre-mrna-to-determine-profibrotic-or-antifibrotic-cell-phenotype
#10
Adam C Midgley, Sebastian Oltean, Vincent Hascall, Emma L Woods, Robert Steadman, Aled O Phillips, Soma Meran
The cell surface protein CD44 is involved in diverse physiological processes, and its aberrant function is linked to various pathologies such as cancer, immune dysregulation, and fibrosis. The diversity of CD44 biological activity is partly conferred by the generation of distinct CD44 isoforms through alternative splicing. We identified an unexpected function for the ubiquitous hyaluronan-degrading enzyme, hyaluronidase 2 (HYAL2), as a regulator of CD44 splicing. Standard CD44 is associated with fibrotic disease, and its production is promoted through serine-arginine-rich (SR) protein-mediated exon exclusion...
November 21, 2017: Science Signaling
https://www.readbyqxmd.com/read/29156766/isobaric-tags-for-relative-and-absolute-quantification-based-proteomic-analysis-of-testis-biopsies-in-rhesus-monkeys-treated-with-transient-scrotal-hyperthermia
#11
Meng Rao, Sha Ma, Shifu Hu, Hui Lei, Yanqing Wu, Yanfei Zhou, Wei Xia, Changhong Zhu
This study aimed to examine the cellular and molecular events that occur in rhesus monkey testes after scrotal hyperthermia. Eight male adult rhesus monkeys were subjected to scrotal hyperthermia at 43°C for 30 min daily for 6 consecutive days. Sperm concentration, reproductive hormones, and testis histology were examined before hyperthermia (day 0), and at 8, 15, 30, 45, 60, 75, and 90 days after the initiation of hyperthermia. iTRAQ-based proteomic analysis was conducted on testicular tissues collected on days 0, 8, and 60 to identify differentially expressed proteins at the early and recovery stages of testicular damage...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155548/site-selective-rna-splicing-nanozyme-dnazyme-and-rtcb-conjugates-on-a-gold-nanoparticle
#12
Jessica R Petree, Kevin Yehl, Kornelia Galior, Roxanne Glazier, Brendan Deal, Khalid Salaita
Modifying RNA through either splicing or editing is a fundamental biological process for creating protein diversity from the same genetic code. Developing novel chemical biology tools for RNA editing has potential to transiently edit genes and to provide a better understanding of RNA biochemistry. Current techniques used to modify RNA include the use of ribozymes, adenosine deaminase and tRNA endonucleases. Herein, we report a nanozyme that is capable of splicing of virtually any RNA stem-loop. This nanozyme is comprised of a gold nanoparticle functionalized with three enzymes: two catalytic DNA strands with ribonuclease function and an RNA ligase...
November 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29153833/structure-of-the-post-catalytic-spliceosome-from-saccharomyces-cerevisiae
#13
Rui Bai, Chuangye Yan, Ruixue Wan, Jianlin Lei, Yigong Shi
Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3.6 Å. The ligated exon is held in the active site through RNA-RNA contacts. Three bases at the 3' end of the 5' exon remain anchored to loop I of U5 small nuclear RNA, and the conserved AG nucleotides of the 3'-splice site (3'SS) are specifically recognized by the invariant adenine of the branch point sequence, the guanine base at the 5' end of the 5'SS, and an adenine base of U6 snRNA...
November 4, 2017: Cell
https://www.readbyqxmd.com/read/29153391/structure-of-a-thermostable-group-ii-intron-reverse-transcriptase-with-template-primer-and-its-functional-and-evolutionary-implications
#14
Jennifer L Stamos, Alfred M Lentzsch, Alan M Lambowitz
Bacterial group II intron reverse transcriptases (RTs) function in both intron mobility and RNA splicing and are evolutionary predecessors of retrotransposon, telomerase, and retroviral RTs as well as the spliceosomal protein Prp8 in eukaryotes. Here we determined a crystal structure of a full-length thermostable group II intron RT in complex with an RNA template-DNA primer duplex and incoming deoxynucleotide triphosphate (dNTP) at 3.0-Å resolution. We find that the binding of template-primer and key aspects of the RT active site are surprisingly different from retroviral RTs but remarkably similar to viral RNA-dependent RNA polymerases...
November 9, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29151899/globular-domain-structure-and-function-of-restriction-like-endonuclease-lines-similarities-to-eukaryotic-splicing-factor-prp8
#15
M Murshida Mahbub, Saiful M Chowdhury, Shawn M Christensen
Background: R2 elements are a clade of early branching Long Interspersed Elements (LINEs). LINEs are retrotransposable elements whose replication can have profound effects on the genomes in which they reside. No crystal or EM structures exist for the reverse transcriptase (RT) and linker regions of LINEs. Results: Using limited proteolysis as a probe for globular domain structure, we show that the protein encoded by the Bombyx mori R2 element has two major globular domains: (1) a small globular domain consisting of the N-terminal zinc finger and Myb motifs, and (2) a large globular domain consisting of the RT, linker, and type II restriction-like endonuclease (RLE)...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29150981/systematic-proteomic-analysis-of-protein-methylation-in-prokaryotes-and-eukaryotes-revealed-distinct-substrate-specificity
#16
Min Zhang, Jun-Yu Xu, Hao Hu, Bang-Ce Ye, Minjia Tan
The studies of protein methylation mainly focus on lysine and arginine residues due to their diverse roles in essential cellular processes from gene expression to signal transduction. Nevertheless, atypical protein methylation occurring on amino acid residues, such as glutamine and glutamic acid, was largely neglected until recently. In addition, the systematic analysis for the distribution of methylation on different amino acids in various species is still lacking, which hinders our understanding of its functional roles...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150525/distinct-rna-unwinding-mechanisms-of-dead-box-and-deah-box-rna-helicase-proteins-in-remodeling-structured-rnas-and-rnps
#17
REVIEW
Benjamin Gilman, Pilar Tijerina, Rick Russell
Structured RNAs and RNA-protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms...
November 17, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29149092/analysis-of-the-roles-of-the-arabidopsis-nmat2-and-pmh2-proteins-provided-with-new-insights-into-the-regulation-of-group-ii-intron-splicing-in-land-plant-mitochondria
#18
Michal Zmudjak, Sofia Shevtsov, Laure D Sultan, Ido Keren, Oren Ostersetzer-Biran
Plant mitochondria are remarkable with respect to the presence of numerous group II introns which reside in many essential genes. The removal of the organellar introns from the coding genes they interrupt is essential for respiratory functions, and is facilitated by different enzymes that belong to a diverse set of protein families. These include maturases and RNA helicases related proteins that function in group II intron splicing in different organisms. Previous studies indicate a role for the nMAT2 maturase and the RNA helicase PMH2 in the maturation of different pre-RNAs in Arabidopsis mitochondria...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29146871/postcatalytic-spliceosome-structure-reveals-mechanism-of-3-splice-site-selection
#19
Max E Wilkinson, Sebastian M Fica, Wojciech P Galej, Christine M Norman, Andrew J Newman, Kiyoshi Nagai
Introns are removed from eukaryotic mRNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7Å cryo-EM structure of the yeast P complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5'-splice site and the branch point adenosine. After the branching reaction protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation...
November 16, 2017: Science
https://www.readbyqxmd.com/read/29146870/structure-of-the-yeast-spliceosomal-postcatalytic-p-complex
#20
Shiheng Liu, Xueni Li, Lingdi Zhang, Jiansen Jiang, Ryan C Hill, Yanxiang Cui, Kirk C Hansen, Z Hong Zhou, Rui Zhao
The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B(act), C, C*, and ILS complexes revealed mechanisms of 5' splice site (ss) recognition, branching, and intron release, but lacked information on 3' ss recognition, exon ligation and release. Here, we report a cryoEM structure of the postcatalytic P complex at 3.3Å resolution, revealing that 3' ss is mainly recognized through non-Watson-Crick basepairing with the 5' ss and branch point. Furthermore, an unidentified protein becomes stably associated with the P complex, securing the 3' exon and potentially regulating Prp22 activity...
November 16, 2017: Science
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