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https://www.readbyqxmd.com/read/29457530/a-new-insight-into-the-classification-of-dusky-thrush-complex-bearings-on-the-phylogenetic-relationships-within-the-turdidae
#1
Yuanqiu Dong, Bo Li, Lizhi Zhou
Dusky thrush complex comprises of two sister species breeding in SC Siberia, which is the member of thrush Turdus from Turdidae. The phylogenetic resolution of Dusky thrush complex remains controversial, and a detailed research is still necessary. In this research, we determined the complete mtDNAs of both species, and estimated phylogenetic trees based on the mtDNA alignment of these and 21 other Turdidae species, to clarify the taxa status of the Dusky thrush complex. The squenced lengths of these three mitochondrial genomes were 16,737, 16,788 and 16,750 bp...
February 18, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29456792/-n-leucinyl-benzenesulfonamides-as-structurally-simplified-leucyl-trna-synthetase-inhibitors
#2
Michael H Charlton, Rihards Aleksis, Adélaïde Saint-Leger, Arya Gupta, Einars Loza, Lluís Ribas de Pouplana, Ilze Kaula, Daina Gustina, Marina Madre, Daina Lola, Kristaps Jaudzems, Grace Edmund, Christopher P Randall, Louise Kime, Alex J O'Neill, Wil Goessens, Aigars Jirgensons, Paul W Finn
N -Leucinyl benzenesulfonamides have been discovered as a novel class of potent inhibitors of E. coli leucyl-tRNA synthetase. The binding of inhibitors to the enzyme was measured by using isothermal titration calorimetry. This provided information on enthalpy and entropy contributions to binding, which, together with docking studies, were used for structure-activity relationship analysis. Enzymatic assays revealed that N -leucinyl benzenesulfonamides display remarkable selectivity for E. coli leucyl-tRNA synthetase compared to S...
February 8, 2018: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29456023/alternative-mode-of-e-site-trna-binding-in-the-presence-of-a-downstream-mrna-stem-loop-at-the-entrance-channel
#3
Yan Zhang, Samuel Hong, Ajchareeya Ruangprasert, Georgios Skiniotis, Christine M Dunham
Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5...
February 8, 2018: Structure
https://www.readbyqxmd.com/read/29455536/resveratrol-s-hidden-hand-a-route-to-optical-detection-of-biomolecular-binding
#4
Subhojyoti Chatterjee, Seth Olsen, Ewan W Blanch, Feng Wang
Resveratrol (RSVL) is a stilbenoid phytoalexin with promised myriad health benefits predominantly attributed to the trans (E) diastereomeric form. A recent study has implicated the Z (cis) diastereomer in human health. This stereoisomer binds with high affinity to human tyrosyl-tRNA synthetase, initiating a downstream cascade that promotes the expression of genes associated with the cellular stress response. We discovered that the non-planar structure of cis-resveratrol conformer possesses certain chiral signals in its simulated vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra...
February 17, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29454993/in-vitro-studies-of-disease-linked-variants-of-human-trna-nucleotidyltransferase-reveal-decreased-thermal-stability-and-altered-catalytic-activity
#5
M Leibovitch, P J Hanic-Joyce, P B M Joyce
Mutations in the human TRNT1 gene encoding tRNA nucleotidyltransferase (tRNA-NT), an essential enzyme responsible for addition of the CCA (cytidine-cytidine-adenosine) sequence to the 3'-termini of tRNAs, have been linked to disease phenotypes including congenital sideroblastic anemia with B-cell immunodeficiency, periodic fevers and developmental delay (SIFD) or retinitis pigmentosa with erythrocyte microcytosis. The effects of these disease-linked mutations on the structure and function of tRNA-NT have not been explored...
February 15, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29454685/genes-involved-in-tolerance-to-osmotic-stress-by-random-mutagenesis-in-cronobacter-malonaticus
#6
Maofeng Zhang, Xiyan Zhang, Liaowang Tong, Yaping Wang, Dexin Ou, Jumei Zhang, Qingping Wu, Yingwang Ye
Cronobacter malonaticus is one of the opportunistic food-borne pathogens in powdered infant formula and has unusual abilities to survive under environmental stresses such as osmotic conditions. However, the genes involved in osmotic stress have received little attention in C. malonaticus. Here, genes involved in osmotic stress were determined in C. malonaticus using a transposon mutagenesis approach. According to the growth of mutants (n = 215) under 5.0% NaCl concentration, the survival of 5 mutants under osmotic stress was significantly decreased compared with that of the wild type strain...
February 14, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29453282/eukaryotic-translation-elongation-factor-2-eef2-catalyzes-reverse-translocation-of-the-eukaryotic-ribosome
#7
Denis Susorov, Nikita Zakharov, Ekaterina Shuvalova, Alexander Ivanov, Tatiana Egorova, Alexey Shuvalov, Ivan N Shatsky, Elena Alkalaeva
During protein synthesis, a ribosome moves along the mRNA template and, using aminoacyl-tRNAs, decodes the template nucleotide triplets to assemble a protein amino acid sequence. This movement is accompanied by shifting of mRNA-tRNA complexes within the ribosome in a process called translocation. In living cells, this process proceeds in a unidirectional manner, bringing the ribosome to the 3'-end of mRNA, and is catalyzed by the GTPase translation elongation factor 2 (EF-G in prokaryotes, eEF2 in eukaryotes)...
February 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29452640/serine-catabolism-by-shmt2-is-required-for-proper-mitochondrial-translation-initiation-and-maintenance-of-formylmethionyl-trnas
#8
Denise R Minton, Minwoo Nam, Daniel J McLaughlin, Jong Shin, Erol C Bayraktar, Samantha W Alvarez, Vladislav O Sviderskiy, Thales Papagiannakopoulos, David M Sabatini, Kıvanç Birsoy, Richard Possemato
Upon glucose restriction, eukaryotic cells upregulate oxidative metabolism to maintain homeostasis. Using genetic screens, we find that the mitochondrial serine hydroxymethyltransferase (SHMT2) is required for robust mitochondrial oxygen consumption and low glucose proliferation. SHMT2 catalyzes the first step in mitochondrial one-carbon metabolism, which, particularly in proliferating cells, produces tetrahydrofolate (THF)-conjugated one-carbon units used in cytoplasmic reactions despite the presence of a parallel cytoplasmic pathway...
February 15, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29452311/phylogenetic-relationships-and-cryptic-species-diversity-in-the-brazilian-egg-brooding-tree-frog-genus-fritziana-mello-leit%C3%A3-o-1937-anura-hemiphractidae
#9
Marina Walker, Mariana L Lyra, Célio F B Haddad
The genus Fritziana (Anura: Hemiphractidae) comprises six described species (F. goeldii, F. ohausi, F. fissilis, F. ulei, F. tonimi, and F. izecksohni) that are endemic to the Brazilian Atlantic Forest. Although the genus has been the subject of studies dealing with its taxonomy, phylogeny, and systematics, there is considerable evidence for cryptic diversity hidden among the species. The present study aims to understand the genetic diversity and phylogenetic relationships among the species of Fritziana, as well as the relationships among populations within species...
February 13, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29450823/nmr-resonance-assignments-of-rnase-p-protein-from-thermotoga-maritima
#10
Danyun Zeng, Benjamin P Brown, Markus W Voehler, Sheng Cai, Nicholas J Reiter
Ribonuclase P (RNase P) is an essential metallo-endonuclease that catalyzes 5' precursor-tRNA (ptRNA) processing and exists as an RNA-based enzyme in bacteria, archaea, and eukaryotes. In bacteria, a large catalytic RNA and a small protein component assemble to recognize and accurately cleave ptRNA and tRNA-like molecular scaffolds. Substrate recognition of ptRNA by bacterial RNase P requires RNA-RNA shape complementarity, intermolecular base pairing, and a dynamic protein-ptRNA binding interface. To gain insight into the binding specificity and dynamics of the bacterial protein-ptRNA interface, we report the backbone and side chain 1 H, 13 C, and 15 N resonance assignments of the hyperthermophilic Thermatoga maritima RNase P protein in solution at 318 K...
February 15, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29449878/complete-chloroplast-genome-of-the-medicinal-plant-amomum-compactum-gene-organization-comparative-analysis-and-phylogenetic-relationships-within-zingiberales
#11
Ming-Li Wu, Qing Li, Jiang Xu, Xi-Wen Li
Background: Amomum compactum is one of the basic species of the traditional herbal medicine amomi fructus rotundus, with great pharmacology effect. The system position of A. compactum is not clear yet, and the introduction of this plant has been hindered by many plant diseases. However, the correlational molecular studies are relatively scarce. Methods: The total chloroplast (cp) DNA was extracted according to previous studies, and then sequenced by 454 GS FLX Titanium platform...
2018: Chinese Medicine
https://www.readbyqxmd.com/read/29449072/merrf-classification-implications-for-diagnosis-and-clinical-trials
#12
REVIEW
Josef Finsterer, Sinda Zarrouk-Mahjoub, John M Shoffner
BACKGROUND: Given the etiologic heterogeneity of disease classification using clinical phenomenology, we employed contemporary criteria to classify variants associated with myoclonic epilepsy with ragged-red fibers (MERRF) syndrome and to assess the strength of evidence of gene-disease associations. Standardized approaches are used to clarify the definition of MERRF, which is essential for patient diagnosis, patient classification, and clinical trial design. METHODS: Systematic literature and database search with application of standardized assessment of gene-disease relationships using modified Smith criteria and of variants reported to be associated with MERRF using modified Yarham criteria...
December 13, 2017: Pediatric Neurology
https://www.readbyqxmd.com/read/29447106/challenges-of-site-specific-selenocysteine-incorporation-into-proteins-by-escherichia-coli
#13
Xian Fu, Dieter Söll, Anastasia Sevostyanova
Selenocysteine (Sec), a rare genetically encoded amino acid with unusual chemical properties, is of great interest for protein engineering. Sec is synthesized on its cognate tRNA (tRNA Sec ) by the concerted action of several enzymes. While all other aminoacyl-tRNAs are delivered to the ribosome by the elongation factor Tu (EF-Tu), Sec-tRNA Sec requires a dedicated factor, SelB. Incorporation of Sec into protein requires recoding of the stop codon UGA aided by a specific mRNA structure, the SECIS element. This unusual biogenesis restricts the use of Sec in recombinant proteins, limiting our ability to study the properties of selenoproteins...
February 15, 2018: RNA Biology
https://www.readbyqxmd.com/read/29444443/kinetics-and-mechanism-of-mammalian-mitochondrial-ribosome-assembly
#14
Daniel F Bogenhagen, Anne G Ostermeyer-Fay, John D Haley, Miguel Garcia-Diaz
Mammalian mtDNA encodes only 13 proteins, all essential components of respiratory complexes, synthesized by mitochondrial ribosomes. Mitoribosomes contain greatly truncated RNAs transcribed from mtDNA, including a structural tRNA in place of 5S RNA as a scaffold for binding 82 nucleus-encoded proteins, mitoribosomal proteins (MRPs). Cryoelectron microscopy (cryo-EM) studies have determined the structure of the mitoribosome, but its mechanism of assembly is unknown. Our SILAC pulse-labeling experiments determine the rates of mitochondrial import of MRPs and their assembly into intact mitoribosomes, providing a basis for distinguishing MRPs that bind at early and late stages in mitoribosome assembly to generate a working model for mitoribosome assembly...
February 13, 2018: Cell Reports
https://www.readbyqxmd.com/read/29444437/mutations-in-cytosine-5-trna-methyltransferases-impact-mobile-element-expression-and-genome-stability-at-specific-dna-repeats
#15
Bianca Genenncher, Zeljko Durdevic, Katharina Hanna, Daniela Zinkl, Mehrpouya Balaghy Mobin, Nevcin Senturk, Bruno Da Silva, Carine Legrand, Clément Carré, Frank Lyko, Matthias Schaefer
The maintenance of eukaryotic genome stability is ensured by the interplay of transcriptional as well as post-transcriptional mechanisms that control recombination of repeat regions and the expression and mobility of transposable elements. We report here that mutations in two (cytosine-5) RNA methyltransferases, Dnmt2 and NSun2, impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila. Loss of Dnmt2 function caused moderate effects under standard conditions, while heat shock exacerbated these effects...
February 13, 2018: Cell Reports
https://www.readbyqxmd.com/read/29440318/monitoring-the-5-methoxycarbonylmethyl-2-thiouridine-mcm5s2u-modification-in-eukaryotic-trnas-via-the-gamma-toxin-endonuclease
#16
Jenna M Lentini, Jillian Ramos, Dragony Fu
The post-transcriptional modification of tRNA at the wobble position is a universal process occurring in all domains of life. In eukaryotes, the wobble uridine of particular tRNAs is transformed to the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification which is critical for proper mRNA decoding and protein translation. However, current methods to detect mcm5s2U are technically challenging and/or require specialized instrumental expertise. Here, we show that gamma-toxin endonuclease from the yeast Kluyveromyces lactis can be used as a probe for assaying mcm5s2U status in the tRNA of diverse eukaryotic organisms ranging from protozoans to mammalian cells...
February 13, 2018: RNA
https://www.readbyqxmd.com/read/29439501/the-roles-of-mitochondrion-in-intergenomic-gene-transfer-in-plants-a-source-and-a-pool
#17
Nan Zhao, Yumei Wang, Jinping Hua
Intergenomic gene transfer (IGT) is continuous in the evolutionary history of plants. In this field, most studies concentrate on a few related species. Here, we look at IGT from a broader evolutionary perspective, using 24 plants. We discover many IGT events by assessing the data from nuclear, mitochondrial and chloroplast genomes. Thus, we summarize the two roles of the mitochondrion: a source and a pool. That is, the mitochondrion gives massive sequences and integrates nuclear transposons and chloroplast tRNA genes...
February 11, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29439212/oxidation-of-translation-factor-ef-tu-inhibits-the-repair-of-photosystem-ii
#18
Haruhiko Jimbo, Rayakorn Yutthanasirikul, Takanori Nagano, Toru Hisabori, Yukako Hihara, Yoshitaka Nishiyama
The repair of photosystem II (PSII) is particularly sensitive to oxidative stress and the inhibition of repair is associated with oxidative damage to the translational elongation system in the cyanobacterium Synechocystis sp. PCC 6803. However, the molecular mechanism of the inhibition of translational elongation remains to be clarified. In a previous study in vitro, we found that EF-Tu, a translation factor that delivers aminoacyl-tRNA to the ribosome, is inactivated by reactive oxygen species via oxidation of Cys82, a single cysteine residue...
February 8, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29438407/the-complete-mitochondrial-genome-of-somanniathelphusa-boyangensis-and-phylogenetic-analysis-of-genus-somanniathelphusa-crustacea-decapoda-parathelphusidae
#19
Xin-Nan Jia, Shu-Xin Xu, Jun Bai, Yi-Fan Wang, Zong-Heng Nie, Chun-Chao Zhu, Yan Wang, Yi-Xiong Cai, Jie-Xin Zou, Xian-Min Zhou
In this study, the authors first obtained the mitochondrial genome of Somanniathelphusa boyangensis. The results showed that the mitochondrial genome is 17,032bp in length, included 13 protein-coding genes, 2 rRNAs genes, 22 tRNAs genes and 1 putative control region, and it has the characteristics of the metazoan mitochondrial genome A+T bias. All tRNA genes display the typical clover-leaf secondary structure except tRNASer(AGN), which has lost the dihydroxyuridine arm. The GenBank database contains the mitochondrial genomes of representatives of approximately 22 families of Brachyura, comprising 56 species, including 4 species of freshwater crab...
2018: PloS One
https://www.readbyqxmd.com/read/29437101/complete-genome-sequence-of-cluster-j-mycobacteriophage-superphikiman
#20
Pratik Pradhan, Sprikena Nako, Trinh Tran, Lavanya S Aluri, Dharman Anandarajan, Niteesha Betini, Shivangi D Bhatt, Swetha Chengalvala, Nicole E Cox, Bela P Delvadia, Aishwary S Desai, Andrew M Devaney, Brenna K Doyle, Arden O Edgerton, Matthew C Erlich, Kevin C Fitzpatrick, Esha A Gajjar, Anjali Ganguly, Ramnik S Gill, Pauline M Good, Nishtha Gupta, Leila M Haddad, Esther J Han, Shelby Jain, Andrew Jiang, Andrew D Jurgielewicz, Devneet K Kainth, Jawhara M Karam, Mallika Kodavatiganti, Sinja J Kriete, Catherine E MacDonald, Josh P Maret, Ashley E Mathew, Maanasa Natrajan, Nusrat M Nishu, Nirali Patel, Pooja D Patel, Shivani Patel, Kaustav Patra, Karima K Rai, Arghyadeep Sarkar, Priyanka Shah, Ravi K Tata, Andrew H Tawfik, Bhavya T Thuremella, Justina Toma, Shika Veera, Vamsee K Vemulapalli, Trevor V Vidas, Katy S Vieira, Gayathri Vijayakumar, Tru A Walor, Clara R White, Brianna M Wong, Shu L Zhao, David W Bollivar, Matthew T McDonald, Ritu R Dalia, Kevin P W Smith, Joy L Little, Susan M R Gurney
Mycobacteriophage Superphikiman is a cluster J bacteriophage which was isolated from soil collected in Philadelphia, PA. Superphikiman has a 109,799-bp genome with 239 predicted genes, including 2 tRNA genes.
February 1, 2018: Genome Announcements
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