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https://www.readbyqxmd.com/read/28718436/trna-modification-is-cancer-having-a-wobble
#1
Francesca Rapino, Sylvain Delaunay, Zhaoli Zhou, Alain Chariot, Pierre Close
Translational control of protein synthesis supports tumor development and progression to metastasis. Wobble tRNA modifications are required during translation elongation and sustain proteome homeostasis. Recent work has highlighted the surprising upregulation of the wobble uridine 34 (U34) tRNA cascade in cancer, which underlies the specific requirement for this pathway in tumor development.
April 2017: Trends in Cancer
https://www.readbyqxmd.com/read/28717435/psoriasis-bulbar-involvement-and-diarrhea-in-late-myoclonic-epilepsy-with-ragged-red-fibers-syndrome-due-to-the-m-8344a-g-trna-lys-mutation
#2
Josef Finsterer, Gabor Geza Kovacs
No abstract text is available yet for this article.
January 5, 2017: Iranian Journal of Neurology
https://www.readbyqxmd.com/read/28716624/mitochondrial-aminoacyl-trna-synthetases-in-human-disease
#3
REVIEW
Marie Sissler, Ligia Elena González-Serrano, Eric Westhof
Dysfunctions in mitochondria - the powerhouses of the cell - lead to several human pathologies. Because mitochondria integrate nuclear and mitochondrial genetic systems, they are richly intertwined with cellular activities. The nucleus-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are key components of the mitochondrial translation apparatus. Mutations in these enzymes predominantly affect the central nervous system (CNS) but also target other organs. Comparable mutations in mt-aaRSs can lead to vastly diverse diseases, occurring at different stages in life, and within different tissues; this represents a confounding issue...
July 14, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28716262/new-genetic-causes-for-complex-hereditary-spastic-paraplegia
#4
Paulo Victor Sgobbi de Souza, Thiago Bortholin, Renan Braido Dias, Marco Antônio Troccoli Chieia, Stênio Burlin, Fernando George Monteiro Naylor, Wladimir Bocca Vieira de Rezende Pinto, Acary Souza Bulle Oliveira
INTRODUCTION: Hereditary Spastic Paraplegia (HSP) represents a complex and heterogeneous group of rare neurodegenerative disorders that share a common clinical feature of weakness and lower limb spasticity that can occur alone or in combination with a constellation of other neurological or systemic signs and symptoms. Although the core clinical feature of weakness and lower limb spasticity is virtually universal, the genetic heterogeneity is almost uncountable with more than 70 genetic forms described so far...
August 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28716227/mitochondrial-trna-genes-are-hotspots-for-mutations-in-a-cohort-of-patients-with-exercise-intolerance-and-mitochondrial-myopathy
#5
Yuanyuan Lu, Danhua Zhao, Sheng Yao, Shiwen Wu, Daojun Hong, Qingqing Wang, Jing Liu, Jan A M Smeitink, Yun Yuan, Zhaoxia Wang
OBJECTIVE: Mitochondrial myopathy (MM) is a relatively rare type of mitochondrial disorder characterized by predominant skeletal muscle involvement. Both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) mutations have been reported as the genetic causes of this disease. Here, we described the clinical and genetic features of a cohort of patients with MM. METHODS: We conducted a retrospective, single center study enrolling 22 patients with clinically and myopathologically diagnosed MM...
August 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28716126/the-effects-of-potato-virus-y-derived-virus-small-interfering-rnas-of-three-biologically-distinct-strains-on-potato-solanum-tuberosum-transcriptome
#6
Lindani Moyo, Shunmugiah V Ramesh, Madhu Kappagantu, Neena Mitter, Vidyasagar Sathuvalli, Hanu R Pappu
BACKGROUND: Potato virus Y (PVY) is one of the most economically important pathogen of potato that is present as biologically distinct strains. The virus-derived small interfering RNAs (vsiRNAs) from potato cv. Russet Burbank individually infected with PVY-N, PVY-NTN and PVY-O strains were recently characterized. Plant defense RNA-silencing mechanisms deployed against viruses produce vsiRNAs to degrade homologous viral transcripts. Based on sequence complementarity, the vsiRNAs can potentially degrade host RNA transcripts raising the prospect of vsiRNAs as pathogenicity determinants in virus-host interactions...
July 17, 2017: Virology Journal
https://www.readbyqxmd.com/read/28715501/diversity-and-distribution-of-nuclease-bacteriocins-in-bacterial-genomes-revealed-using-hidden-markov-models
#7
Connor Sharp, James Bray, Nicholas G Housden, Martin C J Maiden, Colin Kleanthous
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28715256/structural-basis-for-activation-of-an-archaeal-ribonuclease-p-rna-by-protein-cofactors
#8
Makoto Kimura
Ribonuclease P (RNase P) is an endoribonuclease that catalyzes the processing of the 5'-leader sequence of precursor tRNA (pre-tRNA) in all phylogenetic domains. We have found that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. Biochemical characterizations over the past 10 years have revealed that PhoPop5 and PhoRpp30 fold into a heterotetramer and cooperate to activate a catalytic domain (C-domain) in PhopRNA, whereas PhoRpp21 and PhoRpp29 form a heterodimer and function together to activate a specificity domain (S-domain) in PhopRNA...
July 17, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28714696/genetically-encoded-fluorescent-rna-sensor-for-ratiometric-imag-ing-of-microrna-in-living-tumor-cells
#9
Zhan-Ming Ying, Zhan Wu, Bin Tu, Weihong Tan, Jian-Hui Jiang
Light-up RNA aptamers are valuable tools for fluorescence imaging of RNA in living cells and thus for elucidating RNA functions and dynamics. However, no light-up RNA sensor has been reported for imaging of microRNAs (miRs) in mammalian cells. We herein report a novel genetically-encoded RNA sensor for fluorescent imaging of miRs in liv-ing tumor cells using a light-up RNA aptamer which binds to sulforhodamine and separates it from a conjugated contact quencher. Based on the structural switching mechanism characteristic for molecular beacon, we show that the RNA sensor activates high-contrast fluorescence from the sulfor-hodamine-quencher conjugate when its stem-loop respon-sive motif hybridizes with target miR...
July 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28713786/development-of-a-method-to-extract-and-amplify-the-complete-mitogenome-of-some-sparidae-species
#10
Celestina Mascolo, Marina Ceruso, Paolo Sordino, Giuseppe Palma, Aniello Anastasio, Tiziana Pepe
Previous studies showed that fish mitochondrial DNA (mtDNA) is set up by a closed circular molecule of 16-17 kilobases (kb), comprising 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), 13 protein-coding genes and 2 non-coding regions. The analysis of single mtDNA genes, such as Cytb, COI, 16S and 12S, or short segment of them, has been widely used against species substitution in both fresh and processed fish products. The analysis of the complete mitochondrial genome of fishery products allows to better study and characterise fish species...
April 13, 2017: Italian Journal of Food Safety
https://www.readbyqxmd.com/read/28713421/analyses-of-genomic-trna-reveal-presence-of-novel-trnas-in-oryza-sativa
#11
Tapan K Mohanta, Hanhong Bae
Transfer rRNAs are important molecules responsible for the translation event during protein synthesis. tRNAs are widespread found in unicellular to multi-cellular organisms. Analysis of tRNA gene family members in Oryza sativa revealed the presence of 750 tRNA genes distributed unevenly in different chromosomes. The length of O. sativa tRNAs genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. tRNA(Ser) found in chromosome 8 of O. sativa encoded only 66 nucleotides which is the smallest tRNA of O...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28713409/phylogenetic-resolution-in-juglans-based-on-complete-chloroplast-genomes-and-nuclear-dna-sequences
#12
Wenpan Dong, Chao Xu, Wenqing Li, Xiaoman Xie, Yizeng Lu, Yanlei Liu, Xiaobai Jin, Zhili Suo
Walnuts (Juglans of the Juglandaceae) are well-known economically important resource plants for the edible nuts, high-quality wood, and medicinal use, with a distribution from tropical to temperate zones and from Asia to Europe and Americas. There are about 21 species in Juglans. Classification of Juglans at section level is problematic, because the phylogenetic position of Juglans cinerea is disputable. Lacking morphological and DNA markers severely inhibited the development of related researches. In this study, the complete chloroplast genomes and two nuclear DNA regions (the internal transcribed spacer and ubiquitin ligase gene) of 10 representative taxa of Juglans were used for comparative genomic analyses in order to deepen the understanding on the application value of genetic information for inferring the phylogenetic relationship of the genus...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28712493/crispr-cas9-enabled-multiplex-genome-editing-and-its-application
#13
Bastian Minkenberg, Matthew Wheatley, Yinong Yang
The CRISPR/Cas9 system is a prevalent and versatile genome-editing tool of choice for basic and applied biological research. An exchange of a 20-bp spacer sequence in the gRNA can easily reprogram Cas9 to target a different DNA site. By expressing or providing multiple gRNAs, the system also enables multiplex genome editing at high efficiencies. Current approaches for providing multiple gRNAs in vivo include the use of multigene cassettes to express several gRNAs, Csy4-based excision, arrays of crRNAs, ribozyme-flanked gRNAs, tRNA-dependent cleavage of gRNAs, and direct introduction of Cas9 proteins preloaded with different gRNAs...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28711664/complete-genome-sequence-of-bacillus-velezensis-s3-1-a-potential-biological-pesticide-with-plant-pathogen-inhibiting-and-plant-promoting-capabilities
#14
Qing Jin, Qiuyue Jiang, Lei Zhao, Cuizhu Su, Songshuo Li, Fangyi Si, Shanshan Li, Chenhao Zhou, Yonglin Mu, Ming Xiao
Antagonistic soil microorganisms, which are non-toxic, harmless non-pollutants, can effectively reduce the density of pathogenic species by some ways. Bacillus velezensis strain S3-1 was isolated from the rhizosphere soil of cucumber, and was shown to inhibit plant pathogens, promote plant growth and efficiently colonize rhizosphere soils. The strain produced 13 kinds of lipopeptide antibiotics, belonging to the surfactin, iturin and fengycin families. Here, we presented the complete genome sequence of S3-1...
July 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28708455/functionality-of-trnas-encoded-in-a-mobile-genetic-element-from-an-acidophilic-bacterium
#15
Pamela Alamos, Mario Tello, Paula Bustamante, Fernanda Gutiérrez, Amir Shmaryahu, Juan Maldonado, Gloria Levicán, Omar Orellana
The genome of the acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans, strain ATCC 23270, contains 95 predicted tRNA genes. Thirty-six of these genes (all 20 species) are clustered within an actively excising integrative-conjugative element (ICEAfe1). We speculated that these tRNA genes might have a role in adapting the bacterial tRNA pool to the codon usage of ICEAfe1 genes. To answer this question, we carried out theoretical calculations of the global tRNA adaptation index to the entire A. ferrooxidans genome with and without the ICEAfe1 encoded tRNA genes...
July 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28708049/identification-of-two-novel-functional-trna-derived-fragments-induced-in-response-to-respiratory-syncytial-virus-infection
#16
Jiehua Zhou, Shenxuan Liu, Yu Chen, Yu Fu, Alexander J Silver, Mark S Hill, Inhan Lee, Yong Sun Lee, Xiaoyong Bao
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection (LRTI) in children from infancy up to early childhood. Recently, we demonstrated that RSV infection alters cellular small non-coding RNA (sncRNA) expression, most notably the tRNA-derived RNA fragments (tRFs). However, the functions of the tRFs in virus-host interaction are largely unknown. Herein, we examined the role of three RSV-induced tRFs derived from the 5-end of mature tRNAs decoding GlyCCC, LysCTT and CysGCA (named tRF5-GlyCCC, tRF5-LysCTT and tRF5-CysGCA, respectively) in controlling RSV replication...
July 15, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28707320/homology-model-of-the-human-trna-splicing-ligase-rtcb
#17
Argha Nandy, Patricia Saenz-Mendez, Adrienne M Gorman, Afshin Samali, Leif A Eriksson
RtcB is an essential human tRNA ligase required for ligating the 2',3'-cyclic phosphate and 5'-hydroxyl termini of cleaved tRNA halves during tRNA splicing and XBP1 fragments during endoplasmic reticulum stress. Activation of XBP1 has been implicated in various human tumors including breast cancer. Here we present, for the first time, a homology model of human RtcB (hRtcB) in complex with manganese and covalently bound GMP built from the Pyrococcus horikoshii RtcB (bRtcB) crystal structure, PDB ID 4DWQA. The structure is analyzed in terms of stereochemical quality, folding reliability, secondary structure similarity with bRtcB, druggability of the active site binding pocket and its metal-binding microenvironment...
July 13, 2017: Proteins
https://www.readbyqxmd.com/read/28705967/genome-sequence-of-mycobacterium-phage-crystalp
#18
Christine L Fleischacker, Miriam Segura-Totten, Rebecca A Garlena, Deborah Jacobs-Sera, Welkin H Pope, Daniel A Russell, Graham F Hatfull
Mycobacteriophage CrystalP is a newly isolated phage infecting Mycobacterium smegmatis strain mc(2)155. CrystalP has a 76,483-bp genome and is predicted to contain 143 protein-coding and 2 tRNA genes, including repressor and integrase genes consistent with a temperate lifestyle. CrystalP is related to the mycobacteriophages Toto and Kostya and to other Cluster E phages.
July 13, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28704374/spatial-organization-of-the-budding-yeast-genome-in-the-cell-nucleus-and-identification-of-specific-chromatin-interactions-from-multi-chromosome-constrained-chromatin-model
#19
Gamze Gürsoy, Yun Xu, Jie Liang
Nuclear landmarks and biochemical factors play important roles in the organization of the yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C studies are largely recapitulated by model polymer genomes subject to landmark constraints. However, the origin of inter-chromosomal interactions, specific roles of individual landmarks, and the roles of biochemical factors in yeast genome organization remain unclear. Here we describe a multi-chromosome constrained self-avoiding chromatin model (mC-SAC) to gain understanding of the budding yeast genome organization...
July 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28702279/the-utilization-of-selenocysteine-trna-ser-sec-isoforms-is-regulated-in-part-at-the-level-of-translation-in-vitro
#20
Bradley A Carlson, Nirupama Gupta, Mark H Pinkerton, Dolph L Hatfield, Paul R Copeland
The tRNA for the 21st proteinogenic amino acid, selenocysteine, exists in mammalian cells as 2 isoforms differing by a single 2'-O-methylribosyl moiety at position 34 (Um34). These isoforms contain either 5-methoxycarbonylmethyluridine (mcm(5)U) or 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm(5)Um) at position 34. The accumulation of the mcm(5)Um isoform is tightly correlated with the expression of nonessential "stress response" selenoproteins such as glutathione peroxidase 1 (GPX1). The expression of essential selenoproteins, such as thioredoxin reductase 1 (TXNRD1), is not affected by changes in Sec-tRNA([Ser]Sec) isoform accumulation...
2017: Translation
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