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Group II intron

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https://www.readbyqxmd.com/read/29301905/maize-dek37-encodes-a-p-type-ppr-protein-that-affects-cis-splicing-of-mitochondrial-nad2-intron-1-and-seed-development
#1
Dawei Dai, Shengchao Luan, Xiuzu Chen, Qun Wang, Yang Feng, Chenguang Zhu, Weiwei Qi, Rentao Song
Mitochondrial group II introns require the participation of numerous nucleus-encoded general and specific factors to achieve efficient splicing in vivo Pentatricopeptide repeat (PPR) proteins have been implicated in assisting group II intron splicing. Here, we identified and characterized a new maize seed mutant, defective kernel 37 (dek37), which has significantly delayed endosperm and embryo development. Dek37 encodes a classic P-type PPR protein that targets mitochondria. The dek37 mutation causes no detectable DEK37 protein in mutant seeds...
January 4, 2018: Genetics
https://www.readbyqxmd.com/read/29218637/specific-phosphorothioate-substitution-within-domain-6-of-a-group-ii-intron-ribozyme-leads-to-changes-in-local-structure-and-metal-ion-binding
#2
Michèle C Erat, Emina Besic, Michael Oberhuber, Silke Johannsen, Roland K O Sigel
Group II introns are large self-splicing ribozymes that require high amounts of monovalent and divalent metal ions for folding and catalysis under in vitro conditions. Domain 6 of these ribozymes contains a highly conserved adenosine whose 2'-OH acts as a nucleophile during self-cleavage via the branching pathway. We have previously suggested a divalent metal ion that binds to the major groove at the GU wobble pair above the branch-A in a minimal, but active branch domain construct (D6-27) from the yeast mitochondrial intron Sc...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29191215/domestication-of-self-splicing-introns-during-eukaryogenesis-the-rise-of-the-complex-spliceosomal-machinery
#3
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/29187993/phylogeography-of-schizopygopsis-stoliczkai-cyprinidae-in-northwest-tibetan-plateau-area
#4
Kunyuan Wanghe, Yongtao Tang, Fei Tian, Chenguang Feng, Renyi Zhang, Guogang Li, Sijia Liu, Kai Zhao
Schizopygopsis stoliczkai (Cyprinidae, subfamily Schizothoracinae) is one of the major freshwater fishes endemic to the northwestern margin of the Tibetan Plateau. In the current study, we used mitochondrial DNA markers cytochrome b (Cyt b) and 16S rRNA (16S), as well as the nuclear marker, the second intron of the nuclear beta-actin gene (Act2), to uncover the phylogeography of S. stoliczkai. In total, we obtained 74 haplotypes from 403 mitochondrial concatenated sequences. The mtDNA markers depict the phylogenetic structures of S...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29157056/the-intron-landscape-of-the-mtdna-cytb-gene-among-the-ascomycota-introns-and-intron-encoded-open-reading-frames
#5
Tuhin K Guha, Alvan Wai, Sahra-Taylor Mullineux, Georg Hausner
Fungal mitochondrial genes are frequently noted for the presence of introns. These introns are self-splicing and can be assigned to either group I or II introns and they can encode open reading frames (ORFs). This study examines the introns present within the cytochrome b (cytb) gene of ascomycetes fungi. Cytochrome b gene sequences were sampled from GenBank and supplemented with our own data for species of Leptographium and Ophiostoma. Group I introns were encountered most frequently, many encoding either LAGLIDADG or GIY-YIG homing endonucleases (HEs)...
November 20, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29153391/structure-of-a-thermostable-group-ii-intron-reverse-transcriptase-with-template-primer-and-its-functional-and-evolutionary-implications
#6
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...
December 7, 2017: Molecular Cell
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
#7
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/29136295/genome-wide-association-study-identifies-galc-as-susceptibility-gene-for-mucous-membrane-pemphigoid
#8
C D Sadik, J Bischof, N van Beek, A Dieterich, S Benoit, M Sárdy, M Worm, S Meller, R Gläser, D Zillikens, B Homey, J Setterfield, D Minassian, E Schmidt, J Dart, S M Ibrahim
BACKGROUND: Mucous membrane pemphigoid (MMP) is a rare, chronic, and often aggressive subepidermal autoimmune blistering disease potentially affecting several mucous membranes with blisters and secondary erosions and scars. The pathogenesis of MMP is poorly understood, and the contribution of genetic predispositions, other than HLA class II allele variants to MMP, is unknown. OBJECTIVES: The objective of this study is to identify susceptibility genes for MMP in a British cohort of MMP patients...
November 14, 2017: Experimental Dermatology
https://www.readbyqxmd.com/read/29132315/comprehensive-genomic-analysis-of-the-cngc-gene-family-in-brassica-oleracea-novel-insights-into-synteny-structures-and-transcript-profiles
#9
Kaleem U Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A Almoneafy, Raqeeb Ullah, Xue-Liang Ren, Qing-Yao Shu
BACKGROUND: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. RESULTS: In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29109157/an-ultra-processive-accurate-reverse-transcriptase-encoded-by-a-metazoan-group-ii-intron
#10
Chen Zhao, Fei Liu, Anna Marie Pyle
Group II introns and non-LTR retrotransposons encode a phylogenetically-related family of highly processive reverse transcriptases (RTs) that are essential for mobility and persistence of these retroelements. Recent crystallographic studies on members of this RT family have revealed that they are structurally distinct from the retroviral RTs that are typically used in biotechnology. However, quantitative, structure-guided analysis of processivity, efficiency and accuracy of this alternate RT family has been lacking...
November 6, 2017: RNA
https://www.readbyqxmd.com/read/29073095/broad-role-for-ybx1-in-defining-the-small-noncoding-rna-composition-of-exosomes
#11
Matthew J Shurtleff, Jun Yao, Yidan Qin, Ryan M Nottingham, Morayma M Temoche-Diaz, Randy Schekman, Alan M Lambowitz
RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of conventional RNA-sequencing methods. Here we present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to characterize the RNA extracted from HEK293T cell EVs isolated by flotation gradient ultracentrifugation and from exosomes containing the tetraspanin CD63 further purified from the gradient fractions by immunoisolation...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29064513/the-complete-mitochondrial-genome-of-engyodontium-album-and-comparative-analyses-with-ascomycota-mitogenomes
#12
Xiao-Long Yuan, Xin-Xin Mao, Xin-Min Liu, Sen Cheng, Peng Zhang, Zhong-Feng Zhang
Engyodontium album is a widespread pathogen that causes different kinds of dermatoses and respiratory tract diseases in humans and animals. In spite of its perniciousness, the basic genetic and molecular background of this species remains poorly understood. In this study, the mitochondrial genome sequence of E. album was determined using a high-throughput sequencing platform. The circular mitogenome was found to be 28,081 nucleotides in length and comprised of 17 protein-coding genes, 24 tRNA genes, and 2 rRNA genes...
October 23, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29048531/origin-and-spread-of-spliceosomal-introns-insights-from-the-fungal-clade-zymoseptoria
#13
Baojun Wu, Allison I Macielog, Weilong Hao
Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29045488/alseodaphnopsis-a-new-genus-of-lauraceae-based-on-molecular-and-morphological-evidence
#14
Yue-Qing Mo, Lang Li, Jian-Wu Li, Jens G Rohwer, Hsi-Wen Li, Jie Li
An investigation of a questionable species of the genus Alseodaphne led to the discovery of a new genus Alseodaphnopsis H. W. Li & J. Li, gen. nov., separated from Alseodaphne Nees, and a new species Alseodaphnopsis ximengensis H. W. Li & J. Li, sp. nov., endemic to Yunnan province, China. This new species is characterized by having big, axillary, paniculate inflorescences, as well as large, subglobose fruits. Based on DNA sequence data from two gene regions (nuclear ribosomal ITS and LEAFY intron II), we investigate its phylogenetic position within the Persea group...
2017: PloS One
https://www.readbyqxmd.com/read/29036654/detection-of-expanded-rna-repeats-using-thermostable-group-ii-intron-reverse-transcriptase
#15
Samuel T Carrell, Zhenzhi Tang, Sabine Mohr, Alan M Lambowitz, Charles A Thornton
Cellular accumulation of repetitive RNA occurs in several dominantly-inherited genetic disorders. Expanded CUG, CCUG or GGGGCC repeats are expressed in myotonic dystrophy type 1 (DM1), myotonic dystrophy type 2 (DM2), or familial amyotrophic lateral sclerosis, respectively. Expanded repeat RNAs (ER-RNAs) exert a toxic gain-of-function and are prime therapeutic targets in these diseases. However, efforts to quantify ER-RNA levels or monitor knockdown are confounded by stable structure and heterogeneity of the ER-RNA tract and background signal from non-expanded repeats...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28985291/mobile-genetic-elements-and-evolution-of-crispr-cas-systems-all-the-way-there-and-back
#16
Eugene V Koonin, Kira S Makarova
The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-CRISPR-associated proteins (Cas) systems of bacterial and archaeal adaptive immunity show multifaceted evolutionary relationships with at least five classes of mobile genetic elements (MGE). First, the adaptation module of CRISPR-Cas that is responsible for the formation of the immune memory apparently evolved from a Casposon, a self-synthesizing transposon that employs the Cas1 protein as the integrase and might have brought additional cas genes to the emerging immunity loci...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28981788/empty-pericarp11-serves-as-a-factor-for-splicing-of-mitochondrial-nad1-intron-and-is-required-to-ensure-proper-seed-development-in-maize
#17
Xuemei Ren, Zhenyuan Pan, Hailiang Zhao, Junli Zhao, Manjun Cai, Jiang Li, Zuxin Zhang, Fazhan Qiu
Group II introns are common in the mitochondrial genome of higher plant species. The splicing of these introns is a complex process involving the synergistic action of multiple factors. However, few of these factors have been characterized in maize. In this study, we found that the Empty pericarp11 (Emp11) gene, which encodes a P-type pentatricopeptide repeat (PPR) protein, is required for the development of maize seeds. The loss of Emp11 function seriously impairs embryo and endosperm development, resulting in empty pericarp seeds in maize, and alteration in Emp11 expression leads to quantitative variation in kernel size and weight...
July 20, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28977050/angiotensin-converting-enzyme-id-polymorphism-in-patients-with-heart-failure-secondary-to-chagas-disease
#18
Silene Jacinto da Silva, Salvador Rassi, Alexandre da Costa Pereira
BACKGROUND: Changes in the angiotensin-converting enzyme (ACE) gene may contribute to the increase in blood pressure and consequently to the onset of heart failure (HF). The role of polymorphism is very controversial, and its identification in patients with HF secondary to Chagas disease in the Brazilian population is required. OBJECTIVE: To determine ACE polymorphism in patients with HF secondary to Chagas disease and patients with Chagas disease without systolic dysfunction, and to evaluate the relationship of the ACE polymorphism with different clinical variables...
October 2017: Arquivos Brasileiros de Cardiologia
https://www.readbyqxmd.com/read/28959243/rnase-h-as-gene-modifier-driver-of-evolution-and-antiviral-defense
#19
REVIEW
Karin Moelling, Felix Broecker, Giancarlo Russo, Shinichi Sunagawa
Retroviral infections are 'mini-symbiotic' events supplying recipient cells with sequences for viral replication, including the reverse transcriptase (RT) and ribonuclease H (RNase H). These proteins and other viral or cellular sequences can provide novel cellular functions including immune defense mechanisms. Their high error rate renders RT-RNases H drivers of evolutionary innovation. Integrated retroviruses and the related transposable elements (TEs) have existed for at least 150 million years, constitute up to 80% of eukaryotic genomes and are also present in prokaryotes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28942291/t-homoeolog-specific-plasma-membrane-protein-3-nt-t-pmp3-2-in-polyploid-nicotiana-tabacum-shows-conserved-alternative-splicing-derived-from-extant-nicotiana-tomentosiformis-parent
#20
Kumkum Kumari, Vidya Jegadeeson, S Suji, Gayatri Venkataraman, Ajay Parida
Abiotic stress induced plasma membrane protein 3 (PMP3) genes occur as multigene families in plants, coding for hydrophobic proteins. Group I PMP3s code for shorter ORFs while Group II PMP3s code for proteins with C-terminal extensions. Allotetraploid Nicotiana tabacum (SSTT; 2n = 48) derives its parentage from extant ancestors related to Nicotiana sylvestris (SS) and Nicotiana tomentosiformis (TT). Polyploidization triggers complex genetic and epigenetic changes, often leading to homoeolog-specific retention or loss of function, sub-functionalization or neo-functionalization...
October 2017: Plant Physiology and Biochemistry: PPB
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