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Group II intron

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https://www.readbyqxmd.com/read/28528306/the-group-ii-intron-maturase-a-reverse-transcriptase-and-splicing-factor-go-hand-in-hand
#1
REVIEW
Chen Zhao, Anna Marie Pyle
The splicing of group II introns in vivo requires the assistance of a multifunctional intron encoded protein (IEP, or maturase). Each IEP is also a reverse-transcriptase enzyme that enables group II introns to behave as mobile genetic elements. During splicing or retro-transposition, each group II intron forms a tight, specific complex with its own encoded IEP, resulting in a highly reactive holoenzyme. This review focuses on the structural basis for IEP function, as revealed by recent crystal structures of an IEP reverse transcriptase domain and cryo-EM structures of an IEP-intron complex...
May 18, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28495309/group-ii-introns-in-wheat-mitochondria-have-degenerate-structural-features-and-varied-splicing-pathways
#2
Matthew Ngu, Karen Massel, Linda Bonen
Mitochondrial introns in flowering plant genes are virtually all classified as members of the group II ribozyme family although certain structural features have degenerated to varying degrees over evolutionary time. We are interested in the impact that unconventional intron architecture might have on splicing biochemistry in vivo and we have focused in particular on intronic domains V and VI, which for self-splicing introns provide a key component of the catalytic core and the bulged branchpoint adenosine, respectively...
May 8, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28482231/mobile-self-splicing-introns-and-inteins-as-environmental-sensors
#3
REVIEW
Marlene Belfort
Self-splicing introns and inteins are often mobile at the level of the genome. Although these RNA and protein elements, respectively, are generally considered to be selfish parasites, group I and group II introns and inteins can be triggered by environmental cues to splice and/or to mobilize. These cues include stressors such as oxidizing agents, reactive oxygen and nitrogen species, starvation, temperature, osmolarity and DNA damage. Their sensitivity to these stimuli leads to a carefully choreographed dance between the mobile element and its host that is in tune with the cellular environment...
May 5, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28464070/genome-wide-analysis-of-soybean-containing-genes-a-functional-investigation-of
#4
Hui Yang, Guixia Shi, Hongyang Du, Hong Wang, Zhenzhen Zhang, Dezhou Hu, Jiao Wang, Fang Huang, Deyue Yu
Plant-specific () genes play critical roles in various plant growth and development processes. However, the number and characteristics of genes in soybean [ (L.) Merr.] remain unknown. Here, we identified 90 homologous genes in the soybean genome that phylogenetically clustered into two classes (I and II). The majority of the genes were evenly distributed across all 20 soybean chromosomes, and 77 (81.11%) of them were detected in segmental duplicated regions. Furthermore, the exon-intron organization and motif composition for each were analyzed...
March 2017: Plant Genome
https://www.readbyqxmd.com/read/28438387/structural-insights-into-the-mechanism-of-group-ii-intron-splicing
#5
REVIEW
Chen Zhao, Anna Marie Pyle
While the major architectural features and active-site components of group II introns have been known for almost a decade, information on the individual stages of splicing has been lacking. Recent advances in crystallography and cryo-electron microscopy (cryo-EM) have provided major new insights into the structure of intact lariat introns. Conformational changes that mediate the steps of splicing and retrotransposition are being elucidated, revealing the dynamic, highly coordinated motions that are required for group II intron activity...
April 21, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28405733/association-of-il-1%C3%AE-il-1ra-and-fabp1-gene-polymorphisms-with-the-metabolic-features-of-polycystic-ovary-syndrome
#6
Nadia Rashid, Aruna Nigam, Pikee Saxena, S K Jain, Saima Wajid
BACKGROUND: Polycystic ovary syndrome (PCOS), a highly prevalent endocrinopathy is currently being designated as chronic low grade inflammatory state. IL-1β, IL-1Ra and FABP1 are critical mediators of inflammatory processes and are speculated to play a role in the pathogenesis of PCOS. The aim of this study was to study the association of IL-β, IL-1Ra and FABP1 gene polymorphisms with PCOS and related metabolic features. SUBJECTS: 95 PCOS and 45 age matched healthy control subjects were enrolled in this study...
April 12, 2017: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/28369561/ef-1%C3%AE-dna-sequences-indicate-multiple-origins-of-introduced-populations-of-essigella-californica-hemiptera-aphididae
#7
Thomas Théry, Eckehard G Brockerhoff, Angus J Carnegie, Rui Chen, Stephen R Elms, Maurice Hullé, Richard Glatz, Jaime Ortego, Ge-Xia Qiao, Évelyne Turpeau, Colin Favret
Aphids in the pine-feeding Nearctic genus Essigella (Sternorrhyncha, Aphididae, Lachninae) have been introduced in Europe, North Africa, Oceania, and South America. Mitochondrial, nuclear, and endosymbiont DNA sequences of 12 introduced populations from three continents confirm they all belong to Essigella californica (Essig, 1909). Intron sequence variation of the nuclear gene EF-1α has revealed the existence of four distinct groups. Group I gathers one population from China, where the species is newly reported, and several from Europe (France and Italy); Group II is represented by one population from Argentina; Group III includes two populations from Southern Australia with one from New Zealand; and Group IV corresponds to five populations from Eastern and South-Eastern Australia...
March 23, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28346745/emp10-encodes-a-mitochondrial-ppr-protein-that-affects-the-cis-splicing-of-nad2-intron-1-and-seed-development-in-maize
#8
Manjun Cai, Shuzhen Li, Feng Sun, Qin Sun, Hailiang Zhao, Xuemei Ren, Yanxin Zhao, Bao-Cai Tan, Zuxin Zhang, Fazhan Qiu
In higher plants, many mitochondrial genes contain group II-type introns that are removed from RNAs by splicing to produce mature transcripts that are then translated into functional proteins. However, the factors involved in the splicing of mitochondrial introns and their biological functions are not well understood in maize. Here, we isolated an empty pericarp 10 (emp10) mutant and identified the underlying gene by map-based cloning. Emp10 encodes a P-type mitochondria-targeted pentatricopeptide repeat (PPR) protein with 10 PPR motifs...
March 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28346704/the-chloroplast-rna-helicase-ise2-is-required-for-multiple-chloroplast-rna-processing-steps-in-arabidopsis-thaliana
#9
Krzysztof Bobik, Tyra N McCray, Ben Ernest, Jessica C Fernandez, Katharine A Howell, Thomas Lane, Margaret Staton, Tessa M Burch-Smith
INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2 expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2's role in multiple aspects of chloroplast RNA processing beyond group II intron splicing...
March 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28334800/optimization-of-a-novel-biophysical-model-using-large-scale-in-vivo-antisense-hybridization-data-displays-improved-prediction-capabilities-of-structurally-accessible-rna-regions
#10
Jorge Vazquez-Anderson, Mia K Mihailovic, Kevin C Baldridge, Kristofer G Reyes, Katie Haning, Seung Hee Cho, Paul Amador, Warren B Powell, Lydia M Contreras
Current approaches to design efficient antisense RNAs (asRNAs) rely primarily on a thermodynamic understanding of RNA-RNA interactions. However, these approaches depend on structure predictions and have limited accuracy, arguably due to overlooking important cellular environment factors. In this work, we develop a biophysical model to describe asRNA-RNA hybridization that incorporates in vivo factors using large-scale experimental hybridization data for three model RNAs: a group I intron, CsrB and a tRNA. A unique element of our model is the estimation of the availability of the target region to interact with a given asRNA using a differential entropic consideration of suboptimal structures...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28320321/evolution-of-group-i-introns-in-porifera-new-evidence-for-intron-mobility-and-implications-for-dna-barcoding
#11
Astrid Schuster, Jose V Lopez, Leontine E Becking, Michelle Kelly, Shirley A Pomponi, Gert Wörheide, Dirk Erpenbeck, Paco Cárdenas
BACKGROUND: Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II)...
March 20, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28296777/interleukin-1%C3%AE-and-interleukin-1receptor-antagonist-polymorphisms-in-egyptian-children-with-febrile-seizures-a-case-control-study
#12
Salah Al Morshedy, Hosam F Elsaadany, Hany E Ibrahim, Ashraf M Sherif, Mohsen A A Farghaly, Mayy A N Allah, Heba Abouzeid, Shaimaa S A Elashkar, Mohammed E Hamed, Manar M Fathy, Atef M Khalil, Maha A Noah, Mohamed S Hegab, Ahmed R Ahmed, Mustafa I A Hashem, Ahmed A Emam, Heba G Anany, Boshra R Ibrahim, Heba H Gawish, Rehab M Nabil, Lobna Abdel Fattah, Salah F Alsayed
Febrile seizure is the most common seizure disorder of childhood. Of the pro-inflammatory cytokines, interleukin-1 is defined as the first endogenous pyrogen.We designed this study to investigate single-nucleotide polymorphisms (SNPs) situated at positions -31 (C/T), and -511 (C/T) of interleukin-1beta (IL-1β) gene promoter and interleukin-1receptor antagonist (IL-1RA) gene variable number of tandem repeats in intron 2 (VNTR); to determine whether these polymorphisms could be a marker of susceptibility to febrile seizures in Egyptian children and we also measured the serum level of IL-1β to assess its relation to such polymorphisms...
March 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28265619/influence-of-ph-and-mg-ii-on-the-catalytic-core-domain-5-of-a-bacterial-group-ii-intron
#13
M Pechlaner, A Dominguez-Martin, R K O Sigel
RNA molecules fold into complex structures that allow them to perform specific functions. To compensate the relative lack of diversity of functional groups within nucleotides, metal ions work as crucial co-factors. In addition, shifted pKas are observed in RNA, enabling acid-base reactions at ambient pH. The central catalytic domain 5 (D5) hairpin of the Azotobacter vinelandii group II intron undergoes both metal ion binding and pH dependence, presumably playing an important functional role in the ribozyme's reaction...
March 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28157704/overlooked-fancd2-variant-encodes-a-promising-portent-tumor-suppressor-and-alternative-polyadenylation-contributes-to-its-expression
#14
Bing Han, Yihang Shen, Piyan Zhang, Panneerselvam Jayabal, Raymond Che, Jun Zhang, Herbert Yu, Peiwen Fei
Fanconi Anemia (FA) complementation group D2 protein (FANCD2) is the center of the FA tumor suppressor pathway, which has become an important field of investigation in human aging and cancer. Here we report an overlooked central player in the FA pathway, FANCD2 variant 2 (FANCD2-V2), which appears to perform more potent tumor suppressor-function compared to the known variant of FANCD2, namely, FANCD2-V1. Detailed analysis of the FANCD2 gene structure indicated a proximal and distal polyadenylation site (PAS), associated with V2 and V1 transcripts accordingly...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28099513/the-tetraspanin-associated-uroplakins-family-upk2-3-is-evolutionarily-related-to-ptprq-a-phosphotyrosine-phosphatase-receptor
#15
Javier U Chicote, Rob DeSalle, José Segarra, Tung-Tien Sun, Antonio García-España
Uroplakins are a widespread group of vertebrate integral membrane proteins that belong to two different families: UPK1a and UPK1b belong to the large tetraspanin (TSPAN) gene family, and UPK3a, UPK3b, UPK3c, UPK3d, UPK2a and UPK2b form a family of their own, the UPK2/3 tetraspanin-associated family. In a previous study, we reported that uroplakins first appeared in vertebrates, and that uroplakin tetraspanins (UPK1a and UPK1b) should have originated by duplication of an ancestor tetraspanin gene. However, the evolutionary origin of the UPK2/3 family remains unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28087362/clinical-phenotypes-and-outcomes-of-heritable-and-sporadic-pulmonary-veno-occlusive-disease-a-population-based-study
#16
David Montani, Barbara Girerd, Xavier Jaïs, Marilyne Levy, David Amar, Laurent Savale, Peter Dorfmüller, Andrei Seferian, Edmund M Lau, Mélanie Eyries, Jérôme Le Pavec, Florence Parent, Damien Bonnet, Florent Soubrier, Elie Fadel, Olivier Sitbon, Gérald Simonneau, Marc Humbert
BACKGROUND: Bi-allelic mutations of the EIF2AK4 gene cause heritable pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis (PVOD/PCH). We aimed to assess the effect of EIF2AK4 mutations on the clinical phenotypes and outcomes of PVOD/PCH. METHODS: We did a population-based study using clinical, functional, and haemodynamic data from the registry of the French Pulmonary Hypertension Network. We reviewed the clinical data and outcomes from all patients referred to the French Referral Centre (Pulmonary Department, Hospital Kremlin-Bicêtre, University Paris-Sud) with either confirmed or highly probable PVOD/PCH with DNA available for mutation screening (excluding patients with other risk factors of pulmonary hypertension, such as chronic respiratory diseases)...
February 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/27934709/crystal-structures-of-a-group-ii-intron-lariat-primed-for-reverse-splicing
#17
Maria Costa, Hélène Walbott, Dario Monachello, Eric Westhof, François Michel
The 2'-5' branch of nuclear premessenger introns is believed to have been inherited from self-splicing group II introns, which are retrotransposons of bacterial origin. Our crystal structures at 3.4 and 3.5 angstrom of an excised group II intron in branched ("lariat") form show that the 2'-5' branch organizes a network of active-site tertiary interactions that position the intron terminal 3'-hydroxyl group into a configuration poised to initiate reverse splicing, the first step in retrotransposition. Moreover, the branchpoint and flanking helices must undergo a base-pairing switch after branch formation...
December 2, 2016: Science
https://www.readbyqxmd.com/read/27917941/comparative-phylogenomic-analysis-provides-insights-into-tcp-gene-functions-in-sorghum
#18
Aleena Francis, Namrata Dhaka, Mohit Bakshi, Ki-Hong Jung, Manoj K Sharma, Rita Sharma
Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27871768/red-cell-pyruvate-kinase-deficiency-in-spain-a-study-of-15-cases
#19
Laura Montllor, María Del Mar Mañú-Pereira, Esther Llaudet-Planas, Pilar Gómez Ramírez, Julián Sevilla Navarro, Joan Lluís Vives-Corrons
BACKGROUND AND OBJECTIVE: Pyruvate kinase deficiency (PKD) is a rare, inherited disease causing chronic hemolysis and anemia of varying intensity. The genetic heterogeneity of PKD is high and, to this day, over 240 different mutations have been identified. PATIENTS AND METHODS: 15 unrelated patients affected by PKD have been studied. PKLR gene sequencing was performed by SANGER, including the determination of promoter regions, exonic, intronic flanking and 3'UTR...
January 6, 2017: Medicina Clínica
https://www.readbyqxmd.com/read/27819661/dms-mapseq-for-genome-wide-or-targeted-rna-structure-probing-in-vivo
#20
Meghan Zubradt, Paromita Gupta, Sitara Persad, Alan M Lambowitz, Jonathan S Weissman, Silvi Rouskin
Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase...
January 2017: Nature Methods
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