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Group II intron

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https://www.readbyqxmd.com/read/28852596/chloroplast-genome-expansion-by-intron-multiplication-in-the-basal-psychrophilic-euglenoid-eutreptiella-pomquetensis
#1
Nadja Dabbagh, Matthew S Bennett, Richard E Triemer, Angelika Preisfeld
BACKGROUND: Over the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast genome evolution in early evolving Eutreptiales, this study focused on the cpGenome of Eutreptiella pomquetensis, and the spread and peculiarities of introns...
2017: PeerJ
https://www.readbyqxmd.com/read/28827600/facile-single-stranded-dna-sequencing-of-human-plasma-dna-via-thermostable-group-ii-intron-reverse-transcriptase-template-switching
#2
Douglas C Wu, Alan M Lambowitz
High-throughput single-stranded DNA sequencing (ssDNA-seq) of cell-free DNA from plasma and other bodily fluids is a powerful method for non-invasive prenatal testing, and diagnosis of cancers and other diseases. Here, we developed a facile ssDNA-seq method, which exploits a novel template-switching activity of thermostable group II intron reverse transcriptases (TGIRTs) for DNA-seq library construction. This activity enables TGIRT enzymes to initiate DNA synthesis directly at the 3' end of a DNA strand while simultaneously attaching a DNA-seq adapter without end repair, tailing, or ligation...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819820/genome-wide-characterization-of-the-wrky-gene-family-in-radish-raphanus-sativus-l-reveals-its-critical-functions-under-different-abiotic-stresses
#3
Bernard Kinuthia Karanja, Lianxue Fan, Liang Xu, Yan Wang, Xianwen Zhu, Mingjia Tang, Ronghua Wang, Fei Zhang, Everlyne M'mbone Muleke, Liwang Liu
The radish WRKY gene family was genome-widely identified and played critical roles in response to multiple abiotic stresses. The WRKY is among the largest transcription factors (TFs) associated with multiple biological activities for plant survival, including control response mechanisms against abiotic stresses such as heat, salinity, and heavy metals. Radish is an important root vegetable crop and therefore characterization and expression pattern investigation of WRKY transcription factors in radish is imperative...
August 17, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28818345/mobile-group-ii-introns-as-ancestral-eukaryotic-elements
#4
REVIEW
Olga Novikova, Marlene Belfort
The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes...
August 14, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28814522/characterization-of-cis-acting-rna-elements-of-zika-virus-by-using-a-self-splicing-ribozyme-dependent-infectious-clone
#5
Zhong-Yu Liu, Jiu-Yang Yu, Xing-Yao Huang, Hang Fan, Xiao-Feng Li, Yong-Qiang Deng, Xue Ji, Meng-Li Cheng, Qing Ye, Hui Zhao, Jian-Feng Han, Xiao-Ping An, Tao Jiang, Bo Zhang, Yi-Gang Tong, Cheng-Feng Qin
Zika virus (ZIKV) has caused significant outbreaks and epidemics in the Americas recently, raising global concern due to its ability to cause microcephaly and other neurological complications. A stable and efficient infectious clone of ZIKV is urgently needed. However, the instability and toxicity of flavivirus cDNA clones in E. coli hosts has hindered the development of ZIKV infectious clones. Herein, using a novel self-splicing ribozyme-based strategy, we have generated a stable infectious cDNA clone of a contemporary ZIKV strain imported from Venezuela to China in 2016...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28800729/accd-nuclear-transfer-of-platycodon-grandiflorum-and-the-plastid-of-early-campanulaceae
#6
Chang Pyo Hong, Jihye Park, Yi Lee, Minjee Lee, Sin Gi Park, Yurry Uhm, Jungho Lee, Chang-Kug Kim
BACKGROUND: Campanulaceae species are known to have highly rearranged plastid genomes lacking the acetyl-CoA carboxylase (ACC) subunit D gene (accD), and instead have a nuclear (nr)-accD. Plastid genome information has been thought to depend on studies concerning Trachelium caeruleum and genome announcements for Adenophora remotiflora, Campanula takesimana, and Hanabusaya asiatica. RNA editing information for plastid genes is currently unavailable for Campanulaceae. To understand plastid genome evolution in Campanulaceae, we have sequenced and characterized the chloroplast (cp) genome and nr-accD of Platycodon grandiflorum, a basal member of Campanulaceae...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28767121/combined-association-of-presenilin-1-and-apolipoprotein-e-polymorphisms-with-maternal-meiosis-ii-error-in-down-syndrome-births
#7
Pranami Bhaumik, Priyanka Ghosh, Sujay Ghosh, Eleanor Feingold, Umut Ozbek, Biswanath Sarkar, Subrata Kumar Dey
Alzheimer's disease and Down syndrome often exhibit close association and predictively share common genetic risk-factors. Presenilin-1 (PSEN-1) and Apolipoprotein E (APOE) genes are associated with early and late onset of Alzheimer's disease, respectively. Presenilin -1 is involved in faithful chromosomal segregation. A higher frequency of the APOE ε4 allele has been reported among young mothers giving birth to Down syndrome children. In this study, 170 Down syndrome patients, grouped according to maternal meiotic stage of nondisjunction and maternal age at conception, and their parents were genotyped for PSEN-1 intron-8 and APOE polymorphisms...
July 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28760704/determination-of-alpha-2-mrap-gene-polymorphisms-in-nephrolithiasis-patients
#8
Atheer Awad Mehde, Wesen Adel Mehdi, Faridah Yusof, Raha Ahmed Raus, Zaima Azira Zainal Abidin, Hamid Ghazali, Azlina Abd Rahman
BACKGROUND: The intron 5 insertion/deletion polymorphism of Alpha-2-macroglobulin receptor-associated protein gene (Alpha-2-MRAP) has been implicated in numerous diseases. The current study was designed to analyze the association of intron 5 insertion/deletion polymorphism of Alpha-2-MRAP with nephrolithiasis patients. METHODS: PCR was conducted on genomic DNA of patients and control to look for Alpha-2-MRAP insertion/deletion polymorphism. Besides that, serum level of Alpha-2-MRAP, oxidative stress marker myeloperoxidase, Malondialdehyde (MDA), Advanced oxidation protein products (AOPP), and uric acid were determined...
July 29, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28698278/on-the-origin-of-reverse-transcriptase-using-crispr-cas-systems-and-their-hyperdiverse-enigmatic-spacer-repertoires
#9
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
#10
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
#11
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 two ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein-coding genes, and 12 open reading frames. The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions. A total of six introns were present in the smaller U...
July 4, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28655915/multiple-introns-in-a-deep-sea-annelid-decemunciger-ampharetidae-mitochondrial-genome
#12
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
#13
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...
August 1, 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
#14
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. The aim of the present study is to examine the role of Caspase 8 and 3 polymorphisms in the pathogenesis of CAD. CAD patients (n=300) and healthy controls (n=300) were genotyped for polymorphisms in CASP8 (-652 6N del/ins, IVS12-19G>A), CASP3 (rs4647601;G>T) by PCR-RFLP. Splicing defects were determined by HSF...
September 5, 2017: Gene
https://www.readbyqxmd.com/read/28607538/phylogenetic-analysis-of-nuclear-encoded-rna-maturases
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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