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Group II intron

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https://www.readbyqxmd.com/read/28698278/on-the-origin-of-reverse-transcriptase-using-crispr-cas-systems-and-their-hyperdiverse-enigmatic-spacer-repertoires
#1
Sukrit Silas, Kira S Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R Krishnamurthy, Becky Xu Hua Fu, Loren L Hansen, David Wang, Matthew B Sullivan, Andrew Millard, Martha R Clokie, Devaki Bhaya, Alan M Lambowitz, Nikos C Kyrpides, Eugene V Koonin, Andrew Z Fire
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28694820/white-stripe-leaf4-encodes-a-novel-p-type-ppr-protein-required-for-chloroplast-biogenesis-during-early-leaf-development
#2
Ying Wang, Yulong Ren, Kunneng Zhou, Linglong Liu, Jiulin Wang, Yang Xu, Huan Zhang, Long Zhang, Zhiming Feng, Liwei Wang, Weiwei Ma, Yunlong Wang, Xiuping Guo, Xin Zhang, Cailin Lei, Zhijun Cheng, Jianmin Wan
Pentatricopeptide repeat (PPR) proteins comprise a large family in higher plants and perform diverse functions in organellar RNA metabolism. Despite the rice genome encodes 477 PRR proteins, the regulatory effects of PRR proteins on chloroplast development remains unknown. In this study, we report the functional characterization of the rice white stripe leaf4 (wsl4) mutant. The wsl4 mutant develops white-striped leaves during early leaf development, characterized by decreased chlorophyll content and malformed chloroplasts...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28677163/mitochondrial-genomes-of-the-green-macroalga-ulva-pertusa-ulvophyceae-chlorophyta-novel-insights-into-the-evolution-of-mitogenomes-in-the-ulvophyceae
#3
Feng Liu, James T Melton, Yuping Bi
To further understand the trends in the evolution of mitochondrial genomes (mitogenomes or mtDNAs) in the Ulvophyceae, the mitogenomes of two separate thalli of Ulva pertusa were sequenced. Two U. pertusa mitogenomes (Up1 and Up2) were 69,333 bp and 64,602 bp in length. These mitogenomes shared 2 ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein-coding genes (PCGs), and 12 open reading frames (ORFs). The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions...
July 4, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28655915/multiple-introns-in-a-deep-sea-annelid-decemunciger-ampharetidae-mitochondrial-genome
#4
Angelo F Bernardino, Yuanning Li, Craig R Smith, Kenneth M Halanych
Wood falls provide episodic fluxes of energy to the sea floor that are degraded by a species-rich benthic fauna. Part of this rich diversity includes annelid polychaetes but unfortunately, our understanding of such fauna is limited and their genetic variability and evolutionary origins remain poorly known. In this study, we sequenced complete mitochondrial genomes from three congeneric Decemunciger (Ampharetidae) individuals that had colonized multiple wood falls in the deep (~1600 m) NE Pacific Ocean. Mitochondrial gene order within Decemunciger was similar to the three other available Terebellomorpha genomes, consistent with the relatively conserved nature of mitochondrial genomes within annelids...
June 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28648679/structure-determination-of-group-ii-introns
#5
REVIEW
Timothy Wiryaman, Navtej Toor
Group II introns are self-splicing catalytic RNAs that are able to excise themselves from pre-mRNAs using a mechanism identical to that utilized by the spliceosome. Both structural and phylogenetic data support the hypothesis that group II introns and the spliceosome share a common ancestor. Structures of group II introns have given insight into the active site required for the catalysis of RNA splicing. This review outlines crucial aspects of the structure determination of group II introns such as sample preparation and data processing...
June 23, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28633917/polymorphic-variants-of-caspase-genes-8-3-in-the-risk-prediction-of-coronary-artery-disease
#6
Kishore Kumar Gundapaneni, Nivas Shyamala, Rajesh Kumar Galimudi, Keerthi Kupsal, Srilatha Reddy Gantala, Chiranjeevi Padala, Padma Gunda, Mohini Aiyengar Tupurani, Kaushik Puranam, Sanjib Kumar Sahu, Surekha Rani Hanumanth
Apoptosis has been involved in a number of pathological conditions including coronary artery disease (CAD). Caspases (CASP) are important regulators and executioners in both extrinsic and intrinsic apoptotic pathways and play a crucial role in the development and progression of CAD. The aim of the present study is to examine the role of Caspase 8 and 3 polymorphisms in the pathogenesis of CAD. 300 CAD patients and 300 healthy controls were genotyped for polymorphisms in CASP8 (-652 6N del/ins, IVS12-19G>A), CASP3 (rs4647601;G>T) by PCR-RFLP...
June 17, 2017: Gene
https://www.readbyqxmd.com/read/28607538/phylogenetic-analysis-of-nuclear-encoded-rna-maturases
#7
Sunita Malik, K C Upadhyaya, Sm Paul Khurana
Posttranscriptional processes, such as splicing, play a crucial role in gene expression and are prevalent not only in nuclear genes but also in plant mitochondria where splicing of group II introns is catalyzed by a class of proteins termed maturases. In plant mitochondria, there are 22 mitochondrial group II introns. matR, nMAT1, nMAT2, nMAT3, and nMAT4 proteins have been shown to be required for efficient splicing of several group II introns in Arabidopsis thaliana. Nuclear maturases (nMATs) are necessary for splicing of mitochondrial genes, leading to normal oxidative phosphorylation...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28579032/genetic-analyses-of-chinese-isolates-of-toxoplasma-gondii-reveal-a-new-genotype-with-high-virulence-to-murine-hosts
#8
J-M Gao, Y-T Xie, Z-S Xu, H Chen, G Hide, T-B Yang, J-L Shen, D-H Lai, Z-R Lun
A great deal of evidence demonstrates that a strongly clonal population structure of Toxoplasma gondii strains exists in humans and animals in North America and Europe, while the strains from South America are genetically separate and more diverse. Potential differences in virulence between different strains mean that an understanding of strain diversity is important to human and animal health. However, to date, only one predominant genotype, ToxoDB#9 (Chinese I), and a few other genotypes, including ToxoDB#205, have been identified in China...
July 15, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28570666/loose-panicle1-encoding-a-novel-wrky-transcription-factor-regulates-panicle-development-stem-elongation-and-seed-size-in-foxtail-millet-setaria-italica-l-p-beauv
#9
Jishan Xiang, Sha Tang, Hui Zhi, Guanqing Jia, Huajun Wang, Xianmin Diao
Panicle development is an important agronomic trait that aids in determining crop productivity. Foxtail millet and its wild ancestor green foxtail have recently been used as model systems to dissect gene functions. Here, we characterized a recessive mutant of foxtail millet, loose-panicle 1 (lp1), which showed pleiotropic phenotypes, such as a lax primary branching pattern, aberrant branch morphology, semi-dwarfism, and enlarged seed size. The loose panicle phenotype was attributed to increased panicle lengths and decreased primary branch numbers...
2017: PloS One
https://www.readbyqxmd.com/read/28528306/the-group-ii-intron-maturase-a-reverse-transcriptase-and-splicing-factor-go-hand-in-hand
#10
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
#11
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
#12
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
#13
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
#14
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...
June 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
#15
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
#16
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...
June 1, 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
#17
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
#18
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
#19
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
#20
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
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