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Group II intron

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https://www.readbyqxmd.com/read/27917941/comparative-phylogenomic-analysis-provides-insights-into-tcp-gene-functions-in-sorghum
#1
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
#2
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...
November 18, 2016: Medicina Clínica
https://www.readbyqxmd.com/read/27819661/dms-mapseq-for-genome-wide-or-targeted-rna-structure-probing-in-vivo
#3
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...
November 7, 2016: Nature Methods
https://www.readbyqxmd.com/read/27812423/proliferation-of-group-ii-introns-in-the-chloroplast-genome-of-the-green-alga-oedocladium-carolinianum-chlorophyceae
#4
Jean-Simon Brouard, Monique Turmel, Christian Otis, Claude Lemieux
BACKGROUND: The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales...
2016: PeerJ
https://www.readbyqxmd.com/read/27765821/mechanistic-insights-into-the-manganese-dependent-phosphodiesterase-activity-of-yeast-dbr1-with-bis-p-nitrophenylphosphate-and-branched-rna-substrates
#5
Beate Schwer, Fahad Khalid, Stewart Shuman
Saccharomyces cerevisiae Dbr1 is a manganese-dependent RNA debranching enzyme that cleaves the 2'-5' phosphodiester bond of the lariat introns formed during pre-mRNA splicing. Dbr1 is a member of the binuclear metallophosphoesterase enzyme superfamily. We showed previously via alanine scanning that RNA debranching in vivo and in vitro depends on conserved active site residues His13, Asp40, Asn85, His86, His179, His231, and His233. Here, by extending the alanine scan, we added Cys11 to the ensemble of essential active site components...
December 2016: RNA
https://www.readbyqxmd.com/read/27765015/recent-horizontal-transfer-functional-adaptation-and-dissemination-of-a-bacterial-group-ii-intron
#6
Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer...
October 20, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27760804/the-reverse-transcriptase-rna-maturase-protein-matr-is-required-for-the-splicing-of-various-group-ii-introns-in-brassicaceae-mitochondria
#7
Laure D Sultan, Daria Mileshina, Felix Grewe, Katarzyna Rolle, Sivan Abudraham, Paweł Głodowicz, Adnan Khan Niazi, Ido Keren, Sofia Shevtsov, Liron Klipcan, Jan Barciszewski, Jeffrey P Mower, Andre Dietrich, Oren Ostersetzer
Group II introns are large catalytic RNAs that are ancestrally related to nuclear spliceosomal introns. Sequences corresponding to group II RNAs are found in many prokaryotes and are particularly prevalent within plants organellar genomes. Proteins encoded within the introns themselves (maturases) facilitate the splicing of their own host pre-RNAs. Mitochondrial introns in plants have diverged considerably in sequence and have lost their maturases. In angiosperms, only a single maturase has been retained in the mitochondrial DNA: the matR gene found within NADH dehydrogenase 1 (nad1) intron 4...
October 19, 2016: Plant Cell
https://www.readbyqxmd.com/read/27742820/piece-2-0-an-update-for-the-plant-gene-structure-comparison-and-evolution-database
#8
Yi Wang, Ling Xu, Roger Thilmony, Frank M You, Yong Q Gu, Devin Coleman-Derr
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version...
October 13, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27730127/functionality-of-in-vitro-reconstituted-group-ii-intron-rmint1-derived-ribonucleoprotein-particles
#9
Maria D Molina-Sánchez, Fernando M García-Rodríguez, Nicolás Toro
The functional unit of mobile group II introns is a ribonucleoprotein particle (RNP) consisting of the intron-encoded protein (IEP) and the excised intron RNA. The IEP has reverse transcriptase activity but also promotes RNA splicing, and the RNA-protein complex triggers site-specific DNA insertion by reverse splicing, in a process called retrohoming. In vitro reconstituted ribonucleoprotein complexes from the Lactococcus lactis group II intron Ll.LtrB, which produce a double strand break, have recently been studied as a means of developing group II intron-based gene targeting methods for higher organisms...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27726484/forks-in-the-tracks-group-ii-introns-spliceosomes-telomeres-and-beyond
#10
Rajendra Kumar Agrawal, Hong-Wei Wang, Marlene Belfort
Group II introns are large catalytic RNAs that form a ribonucleoprotein (RNP) complex by binding to an intron-encoded protein (IEP). The IEP, which facilitates both RNA splicing and intron mobility, has multiple activities including reverse transcriptase. Recent structures of a group II intron RNP complex and of IEPs from diverse bacteria fuel arguments that group II introns are ancestrally related to eukaryotic spliceosomes as well as to telomerase and viruses. Furthermore, recent structural studies of various functional states of the spliceosome allow us to draw parallels between the group II intron RNP and the spliceosome...
October 11, 2016: RNA Biology
https://www.readbyqxmd.com/read/27709575/use-of-group-ii-intron-technology-for-targeted-mutagenesis-in-chlamydia-trachomatis
#11
Charlotte E Key, Derek J Fisher
Dissecting the contribution of genes to virulence in fulfillment of Molecular Koch's postulates is essential for developing prevention and treatment strategies for bacterial pathogens. This chapter will discuss the application of a targeted, intron-based insertional mutagenesis method for creating mutants in the obligate, intracellular bacterial pathogen Chlamydia trachomatis. The methods employed for intron targeting, mutant selection, and mutant verification will be outlined including available selection markers, gene targeting strategies, and potential pitfalls...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27709573/insertion-of-group-ii-intron-based-ribozyme-switches-into-homing-endonuclease-genes
#12
Tuhin Kumar Guha, Georg Hausner
Fungal mitochondrial genomes act as "reservoirs" for homing endonucleases. These enzymes with their DNA site-specific cleavage activities are attractive tools for genome editing, targeted mutagenesis and gene therapy applications. Herein, we present strategies where homing endonuclease open reading frames (HEases ORFs) are interrupted with group II intron sequences. The ultimate goal is to achieve in vivo expression of HEases that can be regulated by manipulating the splicing efficiency of the HEase ORF-embedded group II introns...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27669820/the-similar-and-different-evolutionary-trends-of-mate-family-occurred-between-rice-and-arabidopsis-thaliana
#13
Lihui Wang, Xiujuan Bei, Jiansheng Gao, Yaxuan Li, Yueming Yan, Yingkao Hu
BACKGROUND: Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection. RESULTS: Forty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies...
September 26, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27651997/genome-wide-identification-and-characterization-of-wrky-gene-family-in-salix-suchowensis
#14
Changwei Bi, Yiqing Xu, Qiaolin Ye, Tongming Yin, Ning Ye
WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow...
2016: PeerJ
https://www.readbyqxmd.com/read/27645995/a-ribonucleoprotein-supercomplex-involved-in-trans-splicing-of-organelle-group-ii-introns
#15
Olga Reifschneider, Christina Marx, Jessica Jacobs, Laxmikanth Kollipara, Albert Sickmann, Dirk Wolters, Ulrich Kück
In the chloroplast of the green alga Chlamydomonas reinhardtii, two discontinuous group II introns, psaA-i1 and psaA-i2, splice in trans, and thus their excision process resembles the nuclear spliceosomal splicing pathway. Here, we address the question whether fragmentation of trans-acting RNAs is accompanied by the formation of a chloroplast spliceosome-like machinery. Using a combination of liquid chromatography-mass spectrometry (LC-MS), size exclusion chromatography, and quantitative RT-PCR, we provide the first characterization of a high molecular weight ribonucleoprotein apparatus participating in psaA mRNA splicing...
October 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27610327/the-diversity-of-mtdna-rns-introns-among-strains-of-ophiostoma-piliferum-ophiostoma-pluriannulatum-and-related-species
#16
Iman M Bilto, Georg Hausner
BACKGROUND: Based on previous studies, it was suspected that the mitochondrial rns gene within the Ophiostomatales is rich in introns. This study focused on a collection of strains representing Ophiostoma piliferum, Ophiostoma pluriannulatum and related species that cause blue-stain; these fungi colonize the sapwood of trees and impart a dark stain. This reduces the value of the lumber. The goal was to examine the mtDNA rns intron landscape for these important blue stain fungi in order to facilitate future annotation of mitochondrial genomes (mtDNA) and to potentially identify mtDNA introns that can encode homing endonucleases which may have applications in biotechnology...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27588750/host-factors-influencing-the-retrohoming-pathway-of-group-ii-intron-rmint1-which-has-an-intron-encoded-protein-naturally-devoid-of-endonuclease-activity
#17
Rafael Nisa-Martínez, María Dolores Molina-Sánchez, Nicolás Toro
Bacterial group II introns are self-splicing catalytic RNAs and mobile retroelements that have an open reading frame encoding an intron-encoded protein (IEP) with reverse transcriptase (RT) and RNA splicing or maturase activity. Some IEPs carry a DNA endonuclease (En) domain, which is required to cleave the bottom strand downstream from the intron-insertion site for target DNA-primed reverse transcription (TPRT) of the inserted intron RNA. Host factors complete the insertion of the intron. By contrast, the major retrohoming pathway of introns with IEPs naturally lacking endonuclease activity, like the Sinorhizobium meliloti intron RmInt1, is thought to involve insertion of the intron RNA into the template for lagging strand DNA synthesis ahead of the replication fork, with possible use of the nascent strand to prime reverse transcription of the intron RNA...
2016: PloS One
https://www.readbyqxmd.com/read/27543605/albino-leaf-2-is-involved-in-the-splicing-of-chloroplast-group-i-and-ii-introns-in-rice
#18
Changhong Liu, Haitao Zhu, Yi Xing, Jianjie Tan, Xionghui Chen, Jianjun Zhang, Haifeng Peng, Qingjun Xie, Zemin Zhang
Chloroplasts play an essential role in plant growth and development through manipulating photosynthesis and the production of hormones and metabolites. Although many genes or regulators involved in chloroplast biogenesis and development have been isolated and characterized, identification of novel components is still lacking. We isolated a rice (Oryza sativa) mutant, termed albino leaf 2 (al2), using genetic screening. Phenotypic analysis revealed that the al2 mutation caused obvious albino leaves at the early developmental stage, eventually leading to al2 seedling death...
October 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27503298/mitochondrion-to-chloroplast-dna-transfers-and-intragenomic-proliferation-of-chloroplast-group-ii-introns-in-gloeotilopsis-green-algae-ulotrichales-ulvophyceae
#19
Monique Turmel, Christian Otis, Claude Lemieux
To probe organelle genome evolution in the Ulvales/Ulotrichales clade, the newly sequenced chloroplast and mitochondrial genomes of Gloeotilopsis planctonica and Gloeotilopsis sarcinoidea (Ulotrichales) were compared with those of Pseudendoclonium akinetum (Ulotrichales) and of the few other green algae previously sampled in the Ulvophyceae. At 105,236 bp, the G planctonica mitochondrial DNA (mtDNA) is the largest mitochondrial genome reported so far among chlorophytes, whereas the 221,431-bp G planctonica and 262,888-bp G sarcinoidea chloroplast DNAs (cpDNAs) are the largest chloroplast genomes analyzed among the Ulvophyceae...
2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27492234/convergent-evolution-of-fern-specific-mitochondrial-group-ii-intron-atp1i361g2-and-its-ancient-source-paralogue-rps3i249g2-and-independent-losses-of-intron-and-rna-editing-among-pteridaceae
#20
Simon Maria Zumkeller, Volker Knoop, Nils Knie
Mitochondrial intron patterns are highly divergent between the major land plant clades. An intron in the atp1 gene, atp1i361g2, is an example for a group II intron specific to monilophytes (ferns). Here, we report that atp1i361g2 is lost independently at least 4 times in the fern family Pteridaceae. Such plant organelle intron losses have previously been found to be accompanied by loss of RNA editing sites in the flanking exon regions as a consequence of genomic recombination of mature cDNA. Instead, we now observe that RNA editing events in both directions of pyrimidine exchange (C-to-U and U-to-C) are retained in atp1 exons after loss of the intron in Pteris argyraea/biaurita and in Actiniopteris and Onychium We find that atp1i361g2 has significant similarity with intron rps3i249g2 present in lycophytes and gymnosperms, which we now also find highly conserved in ferns...
2016: Genome Biology and Evolution
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