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https://www.readbyqxmd.com/read/28338825/modular-organization-of-residue-level-contacts-shape-the-selection-pressure-on-individual-amino-acid-sites-of-ribosomal-proteins
#1
Saurav Mallik, Sudip Kundu
Understanding the molecular evolution of macromolecular complexes in the light of their structure, assembly and stability is of central importance. Here we address how the modular organization of native molecular contacts shapes the selection pressure on individual residue sites of ribosomal complexes. The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino acid-nucleotide contacts (OaantC, one amino acid contacts one or multiple nucleotides, inter-nucleotide contacts are disregarded)...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338820/evolutionary-dynamics-of-regulatory-changes-underlying-gene-expression-divergence-among-saccharomyces-species
#2
Brian P H Metzger, Patricia J Wittkopp, Joseph D Coolon
Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. While previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical restrictions to closely related species and limited comparisons have made this observation difficult to test. To address this problem, we used allele-specific RNA-seq data from Saccharomyces species and hybrids to expand both the evolutionary timescale and number of species in which the evolution of regulatory divergence has been investigated...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338690/a-viscous-solvent-enables-information-transfer-from-gene-length-nucleic-acids-in-a-model-prebiotic-replication-cycle
#3
Christine He, Isaac Gállego, Brandon Laughlin, Martha A Grover, Nicholas V Hud
Many hypotheses concerning the nature of early life assume that genetic information was once transferred through the template-directed synthesis of RNA, before the emergence of coded enzymes. However, attempts to demonstrate enzyme-free, template-directed synthesis of nucleic acids have been limited by 'strand inhibition', whereby transferring information from a template strand in the presence of its complementary strand is inhibited by the stability of the template duplex. Here, we use solvent viscosity to circumvent strand inhibition, demonstrating information transfer from a gene-length template (>300 nt) within a longer (545 bp or 3 kb) duplex...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28336682/molecular-mechanism-of-mrna-repression-in-trans-by-a-proq-dependent-small-rna
#4
Alexandre Smirnov, Chuan Wang, Lisa L Drewry, Jörg Vogel
Research into post-transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and Salmonella enterica has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ-dependent sRNAs are largely unknown...
March 23, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28335739/identification-of-long-non-coding-transcripts-with-feature-selection-a-comparative-study
#5
Giovanna M M Ventola, Teresa M R Noviello, Salvatore D'Aniello, Antonietta Spagnuolo, Michele Ceccarelli, Luigi Cerulo
BACKGROUND: The unveiling of long non-coding RNAs as important gene regulators in many biological contexts has increased the demand for efficient and robust computational methods to identify novel long non-coding RNAs from transcripts assembled with high throughput RNA-seq data. Several classes of sequence-based features have been proposed to distinguish between coding and non-coding transcripts. Among them, open reading frame, conservation scores, nucleotide arrangements, and RNA secondary structure have been used with success in literature to recognize intergenic long non-coding RNAs, a particular subclass of non-coding RNAs...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28335016/trna-derived-small-rnas-target-transposable-element-transcripts
#6
German Martinez, Sarah G Choudury, R Keith Slotkin
tRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are processed by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334955/the-schizosaccharomyces-pombe-ppr-protein-ppr10-associates-with-a-novel-protein-mpa1-and-acts-as-a-mitochondrial-translational-activator
#7
Yirong Wang, Jianhua Yan, Qingzhen Zhang, Xuting Ma, Juan Zhang, Minghui Su, Xiaojun Wang, Ying Huang
The pentatricopeptide repeat (PPR) proteins characterized by tandem repeats of a degenerate 35-amino-acid motif function in all aspects of organellar RNA metabolism, many of which are essential for organellar gene expression. In this study, we report the characterization of a fission yeast Schizosaccharomyces pombe PPR protein, Ppr10 and a novel Ppr10-associated protein, designated Mpa1. The ppr10 deletion mutant exhibits growth defects in respiratory media, and is dramatically impaired for viability during the late-stationary phase...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334881/random-pseuoduridylation-in-vivo-reveals-critical-region-of-escherichia-coli-23s-rrna-for-ribosome-assembly
#8
Margus Leppik, Aivar Liiv, Jaanus Remme
Pseudouridine is the most common modified nucleoside in RNA, which is found in stable RNA species and in eukaryotic mRNAs. Functional analysis of pseudouridine is complicated by marginal effect of its absence. We demonstrate that excessive pseudouridines in rRNA inhibit ribosome assembly. Ten-fold increase of pseudouridines in the 16S and 23S rRNA made by a chimeric pseudouridine synthase leads to accumulation of the incompletely assembled large ribosome subunits. Hyper modified 23S rRNA is found in the r-protein assembly defective particles and are selected against in the 70S and polysome fractions showing modification interference...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334831/the-pentatricopeptide-repeat-protein-mtsf2-stabilizes-a-nad1-precursor-transcript-and-defines-the-3%C3%AE-end-of-its-5%C3%AE-half-intron
#9
Chuande Wang, Fabien Aubé, Noelya Planchard, Martine Quadrado, Céline Dargel-Graffin, Fabien Nogué, Hakim Mireau
RNA expression in plant mitochondria implies a large number of post-transcriptional events in which transcript processing and stabilization are essential. In this study, we analyzed the function of the Arabidopsis mitochondrial stability factor 2 gene (MTSF2) and show that the encoded pentatricopeptide repeat protein is essential for the accumulation of stable nad1 mRNA. The production of mature nad1 requires the assembly of three independent RNA precursors via two trans-splicing reactions. Genetic analyses revealed that the lack of nad1 in mtsf2 mutants results from the specific destabilization of the nad1 exons 2-3 precursor transcript...
March 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334819/comparative-analyses-of-the-thermodynamic-rna-binding-signatures-of-different-types-of-rna-recognition-motifs
#10
Brighton Samatanga, Antoine Cléry, Pierre Barraud, Frédéric H-T Allain, Ilian Jelesarov
RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334744/stabilization-of-rna-hairpins-using-non-nucleotide-linkers-and-circularization
#11
Agnieszka Kiliszek, Leszek Blaszczyk, Ryszard Kierzek, Wojciech Rypniewski
An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334305/variance-component-score-test-for-time-course-gene-set-analysis-of-longitudinal-rna-seq-data
#12
Denis Agniel, Boris P Hejblum
As gene expression measurement technology is shifting from microarrays to sequencing, the statistical tools available for their analysis must be adapted since RNA-seq data are measured as counts. It has been proposed to model RNA-seq counts as continuous variables using nonparametric regression to account for their inherent heteroscedasticity. In this vein, we propose tcgsaseq, a principled, model-free, and efficient method for detecting longitudinal changes in RNA-seq gene sets defined a priori. The method identifies those gene sets whose expression varies over time, based on an original variance component score test accounting for both covariates and heteroscedasticity without assuming any specific parametric distribution for the (transformed) counts...
March 10, 2017: Biostatistics
https://www.readbyqxmd.com/read/28333956/discriminating-between-hur-and-ttp-binding-sites-using-the-k-spectrum-kernel-method
#13
Shweta Bhandare, Debra S Goldberg, Robin Dowell
BACKGROUND: The RNA binding proteins (RBPs) human antigen R (HuR) and Tristetraprolin (TTP) are known to exhibit competitive binding but have opposing effects on the bound messenger RNA (mRNA). How cells discriminate between the two proteins is an interesting problem. Machine learning approaches, such as support vector machines (SVMs), may be useful in the identification of discriminative features. However, this method has yet to be applied to studies of RNA binding protein motifs. RESULTS: Applying the k-spectrum kernel to a support vector machine (SVM), we first verified the published binding sites of both HuR and TTP...
2017: PloS One
https://www.readbyqxmd.com/read/28333132/enzyme-iia-ntr-regulates-salmonella-invasion-via-1-2-propanediol-and-propionate-catabolism
#14
Woongjae Yoo, Dajeong Kim, Hyunjin Yoon, Sangryeol Ryu
Many Proteobacteria possess a nitrogen-metabolic phosphotransferase system (PTS(Ntr)) consisting of EI(Ntr), NPr, and EIIA(Ntr) (encoded by ptsP, ptsO, and ptsN, respectively). The PTS(Ntr) plays diverse regulatory roles, but the substrate phosphorylated by EIIA(Ntr) and its primary functions have not yet been identified. To comprehensively understand the roles of PTS(Ntr) in Salmonella Typhimurium, we compared the whole transcriptomes of wild-type and a ΔptsN mutant. Genome-wide RNA sequencing revealed that 3...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28332825/oligonucleotides-containing-aminated-2-amino-lna-nucleotides-synthesis-and-strong-binding-to-complementary-dna-and-rna
#15
Chenguang Lou, Simone V Samuelsen, Niels Johan Christensen, Birte Vester, Jesper Wengel
Mono- and diaminated 2'-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity and significant nuclease resistance. Molecular modelling suggested that structural stabilization occurs via intrastrand electrostatic attraction between the protonated amino groups of the aminated 2'-amino-LNA monomers and the host oligonucleotide backbone.
March 23, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28332713/the-mitochondrial-pentatricopeptide-repeat-protein-ppr19-is-involved-in-the-stabilization-of-nadh-dehydrogenase-1-transcripts-and-is-crucial-for-mitochondrial-function-and-arabidopsis-thaliana-development
#16
Kwanuk Lee, Ji Hoon Han, Youn-Il Park, Catherine Colas des Francs-Small, Ian Small, Hunseung Kang
Despite the importance of pentatricopeptide repeat (PPR) proteins in organellar RNA metabolism and plant development, the functions of many PPR proteins remain unknown. Here, we determined the role of a mitochondrial PPR protein (At1g52620) comprising 19 PPR motifs, thus named PPR19, in Arabidopsis thaliana. The ppr19 mutant displayed abnormal seed development, reduced seed yield, delayed seed germination, and retarded growth, indicating that PPR19 is indispensable for normal growth and development of Arabidopsis thaliana...
March 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28330874/high-resolution-3d-nmr-structure-of-the-kras-proto-oncogene-promoter-reveals-key-features-of-a-g-quadruplex-involved-in-transcriptional-regulation
#17
Abdelaziz Kerkour, Julien Marquevielle, Stefaniia Ivashchenko, Liliya A Yatsunyk, Jean-Louis Mergny, Gilmar F Salgado
Non-canonical base pairing within guanine-rich DNA and RNA sequences can produce G-quartets, whose stacking leads to the formation of a G-quadruplex (G4). G4s can coexist with canonical duplex DNA in the human genome and have been suggested to suppress gene transcription, and much attention has therefore focused on studying G4s in promotor regions of disease-related genes. For example, the human KRAS proto-oncogene contains a nuclease-hypersensitive element (1) located upstream of the major transcription start site...
March 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28328949/mcpip1-alias-regnase-1-binds-and-cleaves-mrna-of-c-ebp%C3%AE
#18
Barbara Lipert, Mateusz Wilamowski, Andrzej Gorecki, Jolanta Jura
CCAAT/enhancer-binding protein beta (C/EBPβ) is a transcription factor controlling a broad range of genes essential for homeostasis, including genes related to immune functions, inflammation, metabolism and growth. Monocyte chemoattractant protein-1-induced protein 1 (MCPIP1) also called as Regnase-1 is an RNase and has been shown to decrease the stability of short-lived transcripts coding for inflammation-related proteins, including IL-1β, IL-6, IL-2, IL-8, IL-12b, IER-3, c-Rel. We found previously that the half-life of the C/EBPβ transcript is regulated by MCPIP...
2017: PloS One
https://www.readbyqxmd.com/read/28327666/hypoxia-induces-h19-expression-through-direct-and-indirect-hif-1%C3%AE-activity-promoting-oncogenic-effects-in-glioblastoma
#19
Weining Wu, Qi Hu, Er Nie, Tianfu Yu, Youzhi Wu, Tongle Zhi, Kuan Jiang, Feng Shen, Yingyi Wang, Junxia Zhang, Yongping You
H19 expression is elevated in many human tumors including glioblastomas, suggesting an oncogenic role for the long noncoding RNA; yet the upregulation of H19 in glioblastomas remains unclear. Here we report that hypoxia significantly stimulated H19 expression in glioblastoma cell lines, which was related to hypoxia-inducible factors 1α (Hif-1α). Hif-1α promoted H19 expression in U87 and U251 cells. Meanwhile PTEN is an advantageous factor to affect H19 expression, through attenuating Hif-1α stability. Hif-1α also positively correlates with H19 in human glioblastoma samples depending on PTEN status...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327539/diverse-mechanisms-of-sulfur-decoration-in-bacterial-trna-and-their-cellular-functions
#20
REVIEW
Chenkang Zheng, Katherine A Black, Patricia C Dos Santos
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species...
March 22, 2017: Biomolecules
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