keyword
MENU ▼
Read by QxMD icon Read
search

Trna

keyword
https://www.readbyqxmd.com/read/29053825/pdm3-a-pentatricopeptide-repeat-containing-protein-affects-chloroplast-development
#1
Jian Zhang, Jianwei Xiao, Yuqian Li, Bodan Su, Huimin Xu, Xiaoyi Shan, Chengwei Song, Jianbo Xie, Ruili Li, Robert Sharwood
The chloroplast, as the photosynthetic organelle of plants, plays a crucial role in plant development. Extensive studies have been conducted on chloroplast development; however, the related regulatory mechanism still remains elusive. Here, we characterized a mutant with defective chloroplasts in Arabidopsis, termed pigment-defective mutant3 (pdm3), which exhibits a distinct albino phenotype in leaves, eventually leading to pdm3 seedling lethality under autotrophic growth conditions. Electron microscopy demonstrated that the number of thylakoids was reduced and the structure of those thylakoids was disrupted in the pdm3 mutant, which eventually led to the breakdown of chloroplasts...
October 19, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29053243/identification-of-the-biosynthetic-pathway-for-the-antibiotic-bicyclomycin
#2
Jon Patteson, Wenlong Cai, Rachel A Johnson, Kevin Santa Maria, Bo Li
Diketopiperazines (DKPs) are a large group of natural products with diverse structures and biological activities. Bicyclomycin is a broad-spectrum DKP antibiotic with unique structure and function: it contains a highly oxidized bicyclic [4.2.2] ring and is the only known selective inhibitor of the bacterial transcription termination factor, Rho. Here, we identify the biosynthetic gene cluster for bicyclomycin containing six iron-dependent oxidases. We demonstrate that the DKP core is made by a tRNA-dependent cyclodipeptide synthase, and hydroxylations on two unactivated sp3 carbons are performed by two mononuclear iron, α-ketoglutarate-dependent hydroxylases...
October 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/29051555/the-first-characterized-phage-against-a-member-of-the-ecologically-important-sphingomonads-reveals-high-dissimilarity-against-all-other-known-phages
#3
Tue Kjærgaard Nielsen, Alexander Byth Carstens, Patrick Browne, René Lametsch, Horst Neve, Witold Kot, Lars Hestbjerg Hansen
This study describes the first molecular characterization of a bacteriophage infecting a member of the environmentally important Sphingomonadaceae family. Both bacteriophage Lacusarx and its host Sphingobium sp. IP1 were isolated from activated sludge from a wastewater treatment plant. Genome sequencing revealed that the phage genes display little similarity to other known phages, despite a remarkable conservation of the synteny in which the functional genes occur among distantly related phages. Phylogenetic analyses confirmed that Lacusarx represents a hitherto undescribed genus of phages...
October 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29049011/-omics-of-food-borne-gastroenteritis-global-proteomic-and-mutagenic-analysis-of-salmonella-enterica-serovar-enteritidis
#4
Aryashree Arunima, Soujanya D Yelamanchi, Chandrashekhar Padhi, Sangeeta Jaiswal, Daniel Ryan, Bhawna Gupta, Gajanan Sathe, Jayshree Advani, Harsha Gowda, T S Keshava Prasad, Mrutyunjay Suar
Salmonella Enteritidis causes food-borne gastroenteritis by the two type three secretion systems (TTSS). TTSS-1 mediates invasion through intestinal lining, and TTSS-2 facilitates phagocytic survival. The pathogens' ability to infect effectively under TTSS-1-deficient background in host's phagocytes is poorly understood. Therefore, pathobiological understanding of TTSS-1-defective nontyphoidal Salmonellosis is highly important. We performed a comparative global proteomic analysis of the isogenic TTSS-1 mutant of Salmonella Enteritidis (M1511) and its wild-type isolate P125109...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29045449/substitutions-in-conserved-regions-preceding-and-within-the-linker-affect-activity-and-flexibility-of-trnase-zl-the-long-form-of-trnase-z
#5
Makenzie Saoura, Kyla Pinnock, Maria Pujantell-Graell, Louis Levinger
The enzyme tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes 3' trailers from precursor tRNAs, preparing them for CCA addition and aminoacylation. The short form of tRNase Z, tRNase ZS, functions as a homodimer and is found in all prokaryotes and some eukaryotes. The long form, tRNase ZL, related to tRNase ZS through tandem duplication and found only in eukaryotes, possesses ~2,000-fold greater catalytic efficiency than tRNase ZS. tRNase ZL consists of related but diverged amino and carboxy domains connected by a flexible linker (also referred to as a flexible tether) and functions as a monomer...
2017: PloS One
https://www.readbyqxmd.com/read/29045140/conformational-change-in-elongation-factor-tu-involves-separation-of-its-domains
#6
Jonathan Lai, Zhaleh Ghaemi, Zaida Luthey-Schulten
Elongation factor Tu (EF-Tu) is a highly conserved GTPase responsible for supplying the aminoacylated tRNA to the ribosome. Upon binding to the ribosome, EF-Tu undergoes GTP hydrolysis which drives a major conformational change, triggering the release of tRNA to the ribosome. Using a combination of molecular simulation techniques, we studied the transition between the pre- and post-hydrolysis structures through two distinct pathways. We show that the transition free energy is minimum along a non-intuitive pathway, that involves "separation" of the GTP binding domain (Domain 1) from the OB folds (Domains 2 and 3), followed by Domain 1 rotation, and, eventually, locking EF-Tu conformation in the post-hydrolysis state...
October 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/29045133/the-product-of-yersinia-pseudotuberculosis-mcc-operon-is-a-peptide-cytidine-antibiotic-activated-inside-producing-cells-by-the-tldd-e-protease
#7
Darya Tsibulskaya, Olga Mokina, Alexey Kulikovsky, Julia Piskunova, Konstantin Severinov, Marina Serebryakova, Svetlana Dubiley
Microcin C is a heptapeptide-adenylate antibiotic produced by some strains of Escherichia coli. Its peptide part is responsible for facilitated transport inside sensitive cells where it is proteolysed with release of a toxic warhead - a non-hydrolysable aspartamidyl-adenylate, which inhibits aspartyl-tRNA synthetase. Recently, a microcin C homolog from Bacillus amyloliquefaciens containing a longer peptide part modified with carboxymethyl-cytosine instead of adenosine was described but no biological activity of this compound was revealed...
October 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29043143/focal-segmental-glomerulosclerosis-associated-with-mitochondrial-disease
#8
Kenneth Lim, David Steele, Andrew Fenves, Ravi Thadhani, Eliot Heher, Amel Karaa
Primary mitochondrial diseases (MD) are complex, heterogeneous inherited diseases caused by mutations in either the mitochondrial or nuclear DNA. Glomerular diseases in MD have been reported with tRNA mutation m.3243A>G causing a syndrome of mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS). We describe here a case of focal segmental glomerulosclerosis (FSGS) associated with a new tRNA mutation site. A 34-year-old man with a history of living related kidney transplantation, diabetes, hearing loss, and developmental delay presented to the outpatient clinic with complaints of new behavioral difficulties, worsening symptoms, and brain involvement on imaging...
2017: Clin Nephrol Case Stud
https://www.readbyqxmd.com/read/29042505/binding-synergy-as-an-essential-step-for-trna-editing-and-modification-enzyme-co-dependence-in-trypanosoma-brucei
#9
Katherine Mary McKenney, Mary Anne T Rubio, Juan D Alfonzo
Transfer RNAs acquire a variety of naturally occurring chemical modifications during their maturation; these fine-tune their structure and decoding properties in a manner critical for protein synthesis. We recently reported that in the eukaryotic parasite, Trypanosoma brucei, a methylation and deamination event are unexpectedly interconnected, whereby the tRNA adenosine deaminase (TbADAT2/3) and the 3-methylcytosine methyltransferase (TbTrm140) strictly rely on each other for activity, leading to formation of m(3)C and m(3)U at position 32 in several tRNAs...
October 17, 2017: RNA
https://www.readbyqxmd.com/read/29040705/the-mrpp1-mrpp2-complex-is-a-trna-maturation-platform-in-human-mitochondria
#10
Linda Reinhard, Sagar Sridhara, B Martin Hällberg
Mitochondrial polycistronic transcripts are extensively processed to give rise to functional mRNAs, rRNAs and tRNAs; starting with the release of tRNA elements through 5'-processing by RNase P (MRPP1/2/3-complex) and 3'-processing by RNase Z (ELAC2). Here, we show using in vitro experiments that MRPP1/2 is not only a component of the mitochondrial RNase P but that it retains the tRNA product from the 5'-processing step and significantly enhances the efficiency of ELAC2-catalyzed 3'-processing for 17 of the 22 tRNAs encoded in the human mitochondrial genome...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29038765/the-complete-chloroplast-genome-sequence-of-strawberry-fragaria-%C3%A2-%C3%A3-%C3%A2-ananassa-duch-and-comparison-with-related-species-of-rosaceae
#11
Hui Cheng, Jinfeng Li, Hong Zhang, Binhua Cai, Zhihong Gao, Yushan Qiao, Lin Mi
Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa 'Benihoppe' using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences...
2017: PeerJ
https://www.readbyqxmd.com/read/29038757/complete-mitochondrial-genome-sequences-of-the-northern-spotted-owl-strix-occidentalis-caurina-and-the-barred-owl-strix-varia-aves-strigiformes-strigidae-confirm-the-presence-of-a-duplicated-control-region
#12
Zachary R Hanna, James B Henderson, Anna B Sellas, Jérôme Fuchs, Rauri C K Bowie, John P Dumbacher
We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S...
2017: PeerJ
https://www.readbyqxmd.com/read/29035363/crystal-structures-reveal-an-elusive-functional-domain-of-pyrrolysyl-trna-synthetase
#13
Tateki Suzuki, Corwin Miller, Li-Tao Guo, Joanne M L Ho, David I Bryson, Yane-Shih Wang, David R Liu, Dieter Söll
Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNA(Pyl). This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNA(Pyl) recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme...
October 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29035361/continuous-directed-evolution-of-aminoacyl-trna-synthetases
#14
David I Bryson, Chenguang Fan, Li-Tao Guo, Corwin Miller, Dieter Söll, David R Liu
Directed evolution of orthogonal aminoacyl-tRNA synthetases (AARSs) enables site-specific installation of noncanonical amino acids (ncAAs) into proteins. Traditional evolution techniques typically produce AARSs with greatly reduced activity and selectivity compared to their wild-type counterparts. We designed phage-assisted continuous evolution (PACE) selections to rapidly produce highly active and selective orthogonal AARSs through hundreds of generations of evolution. PACE of a chimeric Methanosarcina spp...
October 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29034944/power-of-protein-trna-functional-assembly-against-aberrant-aggregation
#15
Charles Bou-Nader, Ludovic Pecqueur, David Cornu, Murielle Lombard, Manuela Dezi, Magali Nicaise, Christophe Velours, Marc Fontecave, Djemel Hamdane
Understanding the mechanisms of protein oligomerization and aggregation is a major concern for biotechnology and medical purposes. However, significant challenges remain in determining the mechanism of formation of these superstructures and the environmental factors that can precisely modulate them. Notably the role that a functional ligand plays in the process of protein aggregation is largely unexplored. We herein address these issues with an original flavin-dependent RNA methyltransferase (TrmFO) used as a protein model since this protein employs a complex set of cofactors and ligands for catalysis...
October 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29034854/whole-genome-transcriptomics-reveals-global-effects-including-up-regulation-of-francisella-pathogenicity-island-gene-expression-during-active-stringent-response-in-the-highly-virulent-francisella-tularensis-subsp-tularensis-schu-s4
#16
Amber L Murch, Paul J Skipp, Peter L Roach, Petra C F Oyston
During conditions of nutrient limitation bacteria undergo a series of global gene expression changes to survive conditions of amino acid and fatty acid starvation. Rapid reallocation of cellular resources is brought about by gene expression changes coordinated by the signalling nucleotides' guanosine tetraphosphate or pentaphosphate, collectively termed (p)ppGpp and is known as the stringent response. The stringent response has been implicated in bacterial virulence, with elevated (p)ppGpp levels being associated with increased virulence gene expression...
October 16, 2017: Microbiology
https://www.readbyqxmd.com/read/29033456/the-dna-methyltransferase-family-a-versatile-toolkit-for-epigenetic-regulation
#17
REVIEW
Frank Lyko
The DNA methyltransferase (DNMT) family comprises a conserved set of DNA-modifying enzymes that have a central role in epigenetic gene regulation. Recent studies have shown that the functions of the canonical DNMT enzymes - DNMT1, DNMT3A and DNMT3B - go beyond their traditional roles of establishing and maintaining DNA methylation patterns. This Review analyses how molecular interactions and changes in gene copy numbers modulate the activity of DNMTs in diverse gene regulatory functions, including transcriptional silencing, transcriptional activation and post-transcriptional regulation by DNMT2-dependent tRNA methylation...
October 16, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29032651/complete-genome-sequence-of-salmonella-enterica-subsp-enterica-serovar-typhimurium-st1120-isolated-from-swine-feces-in-korea
#18
Seongok Kim, Eunsuk Kim, Soyeon Park, Tae-Wook Hahn, Hyunjin Yoon
Salmonella enterica subsp. enterica serovar Typhimurium, one of the most common food-borne pathogens, is transmitted mainly through contaminated food derived from infected animals. In this study, S. Typhimurium ST1120, an isolate from pig feces in Korea, was subjected to whole genome analysis to understand its genomic features associated with virulence. The genome of ST1120 was found to have a circular chromosome of 4,855,001 bp (GC content 52.2%) and a plasmid of 6,863 bp (GC content 46.0%). This chromosome was predicted to have 4,558 open reading frames (ORFs), 17 pseudogenes, 22 rRNA genes, and 86 tRNA genes...
October 14, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29031721/cdkal1-a-type-2-diabetes-susceptibility-gene-regulates-mitochondrial-function-in-adipose-tissue
#19
Colin J Palmer, Raphael J Bruckner, Joao A Paulo, Lawrence Kazak, Jonathan Z Long, Amir I Mina, Zhaoming Deng, Katherine B LeClair, Jessica A Hall, Shangyu Hong, Peter-James H Zushin, Kyle L Smith, Steven P Gygi, Susan Hagen, David E Cohen, Alexander S Banks
OBJECTIVES: Understanding how loci identified by genome wide association studies (GWAS) contribute to pathogenesis requires new mechanistic insights. Variants within CDKAL1 are strongly linked to an increased risk of developing type 2 diabetes and obesity. Investigations in mouse models have focused on the function of Cdkal1 as a tRNA(Lys) modifier and downstream effects of Cdkal1 loss on pro-insulin translational fidelity in pancreatic β-cells. However, Cdkal1 is broadly expressed in other metabolically relevant tissues, including adipose tissue...
October 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/29031680/soluble-expression-and-purification-of-a-full-length-asparaginyl-trna-synthetase-from-fasciola-gigantica
#20
R Vijayakumar, Timir Tripathi
We report the molecular cloning, expression, and single-step homogeneous purification of a full-length asparaginyl tRNA synthetase (NRS) from Fasciola gigantica (FgNRS). Fasciola gigantica is a parasitic liver fluke of the class Trematoda. It causes fascioliasis that infects the liver of various mammals, including humans. Aminoacyl tRNA synthetases (AARS) catalyze the first step of protein synthesis. They attach an amino acid to its cognate tRNA, forming an amino acid-tRNA complex. The gene that codes for FgNRS was generated by amplification by polymerase chain reaction...
October 12, 2017: Protein Expression and Purification
keyword
keyword
20081
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"