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https://www.readbyqxmd.com/read/28820624/retinopathy-and-optic-atrophy-expanding-the-phenotypic-spectrum-of-pathogenic-variants-in-the-aars2-gene
#1
Jason H Peragallo, Stephanie Keller, Marjo S van der Knaap, Bruno P Soares, Suma P Shankar
BACKGROUND: Optic atrophy may be the sequela of optic nerve injury due to any insult, including isolated and syndromic genetic diseases. Alanyl-tRNA synthetase 2 (AARS2) pathogenic variants have been reported to cause leukodystrophy with ovarian failure, and cardiomyopathy (#615889) as well as combined oxidative phosphorylation deficiency-8 (#614096). We report a young child who presented with decreased vision due to optic atrophy and was found to harbor missense variants in the AARS2 gene expanding the phenotypic expression of the AARS2 gene...
August 18, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28819113/insights-into-the-role-of-endonuclease-v-in-rna-metabolism-in-trypanosoma-brucei
#2
Daniel García-Caballero, Guiomar Pérez-Moreno, Antonio M Estévez, Luis Miguel Ruíz-Pérez, Antonio E Vidal, Dolores González-Pacanowska
Inosine may arise in DNA as a result of oxidative deamination of adenine or misincorporation of deoxyinosine triphosphate during replication. On the other hand, the occurrence of inosine in RNA is considered a normal and essential modification induced by specific adenosine deaminases acting on mRNA and tRNA. In prokaryotes, endonuclease V (EndoV) can recognize and cleave inosine-containing DNA. In contrast, mammalian EndoVs preferentially cleave inosine-containing RNA, suggesting a role in RNA metabolism for the eukaryotic members of this protein family...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28816616/transfer-rna-mediated-enhancement-of-ribosomal-proteins-s6-kinases-signalling-for-cell-proliferation
#3
Nam Hoon Kwon, Mi Ran Lee, Jiwon Kong, Seung Kyun Park, Byung Joon Hwang, Byung Gyu Kim, Eun-Shin Lee, Hyeong-Gon Moon, Sunghoon Kim
While transfer RNAs (tRNAs) are known to transport amino acids to ribosome, new functions are being unveiled from tRNAs and their fragments beyond protein synthesis. Here we show that phosphorylation of 90-kDa RPS6K (ribosomal proteins S6 kinase) was enhanced by tRNA(Leu) overexpression under amino acids starvation condition. The phosphorylation of 90-kDa RPS6K was decreased by siRNA specific to tRNA(Leu) and was independent to mTOR (mammalian target of rapamycin) signalling. Among the 90-kDa RPS6K family, RSK1 (ribosomal S6 kinase 1) and MSK2 (mitogen-and stress-activated protein kinase 2) were the major kinases phosphorylated by tRNA(Leu) overexpression...
August 17, 2017: RNA Biology
https://www.readbyqxmd.com/read/28816600/deciphering-the-trna-dependent-lipid-aminoacylation-systems-in-bacteria-novel-components-and-structural-advances
#4
Rachel N Fields, Hervé Roy
tRNA-dependent addition of amino acids to lipids on the outer surface of the bacterial membrane results in decreased effectiveness of antimicrobials such as cationic antimicrobial peptides (CAMPs) that target the membrane, and increased virulence of several pathogenic species. After a brief introduction to CAMPs and the various bacterial resistance mechanisms used to counteract these compounds, this review focuses on recent advances in tRNA-dependent pathways for lipid modification in bacteria. Phenotypes associated with amino acid lipid modifications and regulation of their expression will also be discussed...
August 17, 2017: RNA Biology
https://www.readbyqxmd.com/read/28815535/history-discovery-and-classification-of-lncrnas
#5
Julien Jarroux, Antonin Morillon, Marina Pinskaya
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28814526/hiv-1-exploits-dynamic-multi-aminoacyl-trna-synthetase-complex-to-enhance-viral-replication
#6
Alice A Duchon, Corine St-Gelais, Nathan Titkemeier, Joshua Hatterschide, Li Wu, Karin Musier-Forsyth
A hallmark of retroviruses such as human immunodeficiency virus type 1 (HIV-1) is reverse transcription of genomic RNA to DNA, a process that is primed by cellular tRNAs. HIV-1 recruits human tRNA(Lys3) to serve as the reverse transcription primer via an interaction between lysyl-tRNA synthetase (LysRS) and the HIV-1 Gag polyprotein. LysRS is normally sequestered in a multi-aminoacyl-tRNA synthetase complex (MSC). Previous studies demonstrated that components of the MSC can be mobilized in response to certain cellular stimuli, but how LysRS is redirected from the MSC to viral particles for packaging is unknown...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28814300/increasing-on-target-cleavage-efficiency-for-crispr-cas9-induced-large-fragment-deletion-in-myxococcus-xanthus
#7
Ying-Jie Yang, Ye Wang, Zhi-Feng Li, Ya Gong, Peng Zhang, Wen-Chao Hu, Duo-Hong Sheng, Yue-Zhong Li
BACKGROUND: The CRISPR/Cas9 system is a powerful tool for genome editing, in which the sgRNA binds and guides the Cas9 protein for the sequence-specific cleavage. The protocol is employable in different organisms, but is often limited by cell damage due to the endonuclease activity of the introduced Cas9 and the potential off-target DNA cleavage from incorrect guide by the 20 nt spacer. RESULTS: In this study, after resolving some critical limits, we have established an efficient CRISPR/Cas9 system for the deletion of large genome fragments related to the biosynthesis of secondary metabolites in Myxococcus xanthus cells...
August 16, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28812932/celebrating-wobble-decoding-half-a-century-and-still-much-is-new
#8
Paul F Agris, Emily R Eruysal, Amithi Narendran, Ville Y P Väre, Sweta Vangaveti, Srivathsan V Ranganathan
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons...
August 16, 2017: RNA Biology
https://www.readbyqxmd.com/read/28809560/recombinant-macrocyclic-lanthipeptides-incorporating-non-canonical-amino-acids
#9
Claudio Zambaldo, Xiaozhou Luo, Angad P Mehta, Peter G Schultz
Nisin is a complex lanthipeptide that has broad spectrum antibacterial activity. In efforts to broaden the structural diversity of this ribosomally synthesized lantibiotic, we now report the recombinant expression of Nisin variants that incorporate noncanonical amino acids (ncAAs) at discrete positions. This is achieved by expressing the nisA structural gene, cyclase (nisC) and dehydratase (nisB), together with an orthogonal nonsense suppressor tRNA/aminoacyl-tRNA synthetase pair in Escherichia coli. A number of ncAAs with novel chemical reactivity were genetically incorporated into NisA, including an α-chloroacetamide-containing ncAA that allowed for the expression of Nisin variants with novel macrocyclic topologies...
August 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28808384/molecular-authentication-of-the-traditional-medicinal-plant-lakshman-booti-smithia-conferta-sm-and-its-adulterants-through-dna-barcoding
#10
Suraj D Umdale, Parthraj R Kshirsagar, Manoj M Lekhak, Nikhil B Gaikwad
BACKGROUND: Smithia conferta Sm. is an annual herb widely used in Indian traditional medical practice and commonly known as "Lakshman booti" in Sanskrit. Morphological resemblance among the species of genus Smithia Aiton. leads to inaccurate identification and adulteration. This causes inconsistent therapeutic effects and also affects the quality of herbal medicine. AIM: This study aimed to generate potential barcode for authentication of S. conferta and its adulterants through DNA barcoding technique...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28808133/the-rph-1-encoded-truncated-rnase-ph-protein-inhibits-rnase-p-maturation-of-pre-trnas-with-short-leader-sequences-in-the-absence-of-rpph
#11
Katherine E Bowden, Nicholas S Wiese, Tariq Perwez, Bijoy K Mohanty, Sidney R Kushner
RNase PH, encoded by the rph gene, is a 3' → 5' exoribonuclease that in E. coli participates primarily in the 3' maturation of pre-tRNAs and the degradation of ribosomal RNA (rRNA) in stationary phase cells. Interestingly, the routinely used laboratory strains of MG1655 and W3110 have naturally acquired the rph-1 allele encoding a truncated, catalytically inactive RNase PH protein, which is widely assumed to be benign. Contrary to this assumption, we show that rph-1 encoded Rph-1 protein inhibits RNase P mediated 5' end maturation of primary pre-tRNAs with leaders < 5 nucleotides in the absence of RppH, an RNA pyrophosphohydrolase...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28808125/insights-into-substrate-promiscuity-of-human-seryl-trna-synthetase
#12
Kaitlyn M Holman, Anupama K Puppala, Jonathan W Lee, Hyun Lee, Miljan Simonovic
Seryl-tRNA synthetase (SerRS) attaches L-serine to the cognate serine tRNA (tRNA(Ser)) and the non-cognate selenocysteine tRNA (tRNA(Sec)). The latter activity initiates the anabolic cycle of selenocysteine (Sec), proper decoding of an in-frame Sec UGA codon, and synthesis of selenoproteins across all domains of life. While the accuracy of SerRS is important for overall proteome integrity, it is its substrate promiscuity that is vital for the integrity of the selenoproteome. This raises a question as to what elements in the two tRNA species, harboring different anticodon sequences and adopting distinct folds, facilitate aminoacylation by a common aminoacyl-tRNA synthetase...
August 14, 2017: RNA
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#13
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28803904/complete-mitochondrial-genomes-of-triodontophorus-serratus-and-triodontophorus-nipponicus-and-their-comparison-with-triodontophorus-brevicauda
#14
Jun-Feng Gao, Guo-Hua Liu, Hong Duan, Yuan Gao, Yan Zhang, Qiao-Cheng Chang, Ming Fang, Chun-Ren Wang
Triodontophorus serratus and Triodontophorus nipponicus are two of the most common nematodes inhabiting in the large intestine of horse. In the present study, the complete mitochondrial (mt) genome sequences of T. serratus and T. nipponicus have been determined. The mt genomes of T. serratus and T. nipponicus are circular molecules with 13,794 bp and 13,701 bp in size, respectively. These circular mt genomes encode 36 genes, including 12 protein-coding genes, two rRNA genes and 22 tRNA genes. All of these genes are transcribed in the same direction and gene arrangements are consistent with that of gene arrangement 3 (GA3-type)...
August 10, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28802668/two-novel-lncrnas-discovered-in-human-mitochondrial-dna-using-pacbio-full-length-transcriptome-data
#15
Shan Gao, Xiaoxuan Tian, Hong Chang, Yu Sun, Zhenfeng Wu, Zhi Cheng, Pengzhi Dong, Qiang Zhao, Jishou Ruan, Wenjun Bu
In this study, we introduced a general framework to use PacBio full-length transcriptome sequencing for the investigation of mitochondrial RNAs. As a result, we produced the first full-length human mitochondrial transcriptome based on the public PacBio data and characterized the human mitochondrial transcriptome with more comprehensive and accurate information. Other results included the determination of the H-strand primary transcript, the identification of ND5/ND6AS/tRNA(Glu)AS, the discovery of palindrome small RNAs and the construction of "cleavage" model...
August 9, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28801221/the-aminoacyl-trna-synthetases-had-only-a-marginal-role-in-the-origin-of-the-organization-of-the-genetic-code-evidence-in-favor-of-the-coevolution-theory
#16
Massimo Di Giulio
The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which - this theory - would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been...
August 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28800729/accd-nuclear-transfer-of-platycodon-grandiflorum-and-the-plastid-of-early-campanulaceae
#17
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/28797100/mapping-the-contact-surfaces-in-the-lamin-a-aimp3-complex-by-hydrogen-deuterium-exchange-ft-icr-mass-spectrometry
#18
Yeqing Tao, Pengfei Fang, Sunghoon Kim, Min Guo, Nicolas L Young, Alan G Marshall
Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28794438/complete-mitochondrial-genomes-of-anopheles-stephensi-and-an-dirus-and-comparative-evolutionary-mitochondriomics-of-50-mosquitoes
#19
You-Jin Hao, Yi-Lin Zou, Yi-Ran Ding, Wen-Yue Xu, Zhen-Tian Yan, Xu-Dong Li, Wen-Bo Fu, Ting-Jing Li, Bin Chen
To better understand the phylogeny and evolution of mosquitoes, the complete mitochondrial genome (mitogenome) of Anopheles stephensi and An. dirus were sequenced and annotated, and a total of 50 mosquito mitogenomes were comparatively analyzed. The complete mitogenome of An. stephensi and An. dirus is 1,5371 bp and 1,5406 bp long, respectively. The main features of the 50 mosquito mitogenomes are conservative: 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, positive AT-skew and negative GC-skew...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28793268/characterizing-expression-and-processing-of-precursor-and-mature-human-trnas-by-hydro-trnaseq-and-par-clip
#20
Tasos Gogakos, Miguel Brown, Aitor Garzia, Cindy Meyer, Markus Hafner, Thomas Tuschl
The participation of tRNAs in fundamental aspects of biology and disease necessitates an accurate, experimentally confirmed annotation of tRNA genes and curation of tRNA sequences. This has been challenging because RNA secondary structure, nucleotide modifications, and tRNA gene multiplicity complicate sequencing and mapping efforts. To address these issues, we developed hydro-tRNAseq, a method based on partial alkaline RNA hydrolysis that generates fragments amenable for sequencing. To identify transcribed tRNA genes, we further complemented this approach with photoactivatable crosslinking and immunoprecipitation (PAR-CLIP) of SSB/La, a conserved protein involved in pre-tRNA processing...
August 8, 2017: Cell Reports
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