2016 update of the PRIDE database and its related tools
(Source: Nucleic Acids Research)
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Vizcaino, J. A., Csordas, A., del-Toro, N., Dianes, J. A., Griss, J., Lavidas, I., Mayer, G., Perez-Riverol, Y., Reisinger, F., Ternent, T., Xu, Q.-W., Wang, R., Hermjakob, H. Tags: Corrigendum Source Type: research
A direct view of the complex multi-pathway folding of telomeric G-quadruplexes
G-quadruplexes (G4s) are DNA secondary structures that are capable of forming and function in vivo. The propensity of G4s to exhibit extreme polymorphism and complex dynamics is likely to influence their cellular function, yet a clear microscopic picture of their folding process is lacking. Here we employed single-molecule FRET microscopy to obtain a direct view of the folding and underlying conformational dynamics of G4s formed by the human telomeric sequence in potassium containing solutions. Our experiments allowed detecting several folded states that are populated in the course of G4 folding and determining their foldi...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Aznauryan, M., Sondergaard, S., Noer, S. L., Schiott, B., Birkedal, V. Tags: Structural Biology Source Type: research
Nucleic acid clamp-mediated recognition and stabilization of the physiologically relevant MYC promoter G-quadruplex
The MYC proto-oncogene is upregulated, often at the transcriptional level, in ~80% of all cancers. MYC's promoter is governed by a higher order G-quadruplex (G4) structure in the NHE III1 region. Under a variety of conditions, multiple isoforms have been described to form from the first four continuous guanine runs (G41–4) predominating under the physiologically relevant supercoiled conditions. In the current study, short oligonucleotides complementing the 5'- and 3'-regions flanking the G4 have been connected by an abasic linker to form G4 clamps, varying both linker length and G4 isoform being targeted. Clamp A wit...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Hao, T., Gaerig, V. C., Brooks, T. A. Tags: Structural Biology Source Type: research
Folding and misfolding pathways of G-quadruplex DNA
G-quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. For human telomeric (hTel) sequences containing the d((GGGTTA)3GGG) core, K+ binding affinity and cooperativity strongly depends on the chosen construct. The shortest sequences bind only one K+ at low KCl concentration, and this 2-quartet G-quadruplex is antiparallel. Flanking bases increase the K+ binding cooperativity. To decipher th...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Marchand, A., Gabelica, V. Tags: Structural Biology Source Type: research
S-Geranyl-2-thiouridine wobble nucleosides of bacterial tRNAs; chemical and enzymatic synthesis of S-geranylated-RNAs and their physicochemical characterization
Recently, highly lipophilic S-geranylated derivatives of 5-methylaminomethyl-2-thiouridine (mnm5geS2U) and 5-carboxymethylaminomethyl-2-thiouridine (cmnm5geS2U) were found at the first (wobble) anticodon position in bacterial tRNAs specific for Lys, Glu and Gln. The function and cellular biogenesis of these unique tRNAs remain poorly understood. Here, we present one direct and two post-synthetic chemical routes for preparing model geS2U-RNAs. Our experimental data demonstrate that geS2U-RNAs are more lipophilic than their parent S2U-RNAs as well as non-modified U-RNAs. Thermodynamic studies revealed that the S-geranyl-2-th...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Sierant, M., Leszczynska, G., Sadowska, K., Dziergowska, A., Rozanski, M., Sochacka, E., Nawrot, B. Tags: RNA Source Type: research
A deafness-associated tRNAAsp mutation alters the m1G37 modification, aminoacylation and stability of tRNAAsp and mitochondrial function
In this report, we investigated the pathogenic mechanism underlying the deafness-associated mitochondrial(mt) tRNAAsp 7551A > G mutation. The m.7551A > G mutation is localized at a highly conserved nucleotide(A37), adjacent (3') to the anticodon, which is important for the fidelity of codon recognition and stabilization in functional tRNAs. It was anticipated that the m.7551A > G mutation altered the structure and function of mt-tRNAAsp. The primer extension assay demonstrated that the m.7551A > G mutation created the m1G37 modification of mt-tRNAAsp. Using cybrid cell lines generated by transferring mitochondr...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Wang, M., Peng, Y., Zheng, J., Zheng, B., Jin, X., Liu, H., Wang, Y., Tang, X., Huang, T., Jiang, P., Guan, M.-X. Tags: RNA Source Type: research
Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease
In this study, we show that several human vU1 genes are specifically upregulated in stem cells and participate in the regulation of cell fate decisions. Significantly, ectopic expression of vU1 genes in human skin fibroblasts leads to increases in levels of key pluripotent stem cell mRNA markers, including NANOG and SOX2. These results reveal an important role for vU1s in the control of key regulatory networks orchestrating the transitions between stem cell maintenance and differentiation. Moreover, vU1 expression varies inversely with U1 expression during differentiation and cell re-programming and this pattern of express...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Vazquez-Arango, P., Vowles, J., Browne, C., Hartfield, E., Fernandes, H. J. R., Mandefro, B., Sareen, D., James, W., Wade-Martins, R., Cowley, S. A., Murphy, S., O'Reilly, D. Tags: RNA Source Type: research
tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast
Using budding yeast, we investigated a negative interaction network among genes for tRNA modifications previously implicated in anticodon-codon interaction: 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U34: ELP3, URM1), pseudouridine (38/39: DEG1) and cyclic N6-threonyl-carbamoyl-adenosine (ct6A37: TCD1). In line with functional cross talk between these modifications, we find that combined removal of either ct6A37 or 38/39 and mcm5U34 or s2U34 results in morphologically altered cells with synthetic growth defects. Phenotypic suppression by tRNA overexpression suggests that these defects are caused by malfunction of tRNA...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Klassen, R., Ciftci, A., Funk, J., Bruch, A., Butter, F., Schaffrath, R. Tags: RNA Source Type: research
Nuclear poly(A)-binding protein aggregates misplace a pre-mRNA outside of SC35 speckle causing its abnormal splicing
A short abnormal polyalanine expansion in the polyadenylate-binding protein nuclear-1 (PABPN1) protein causes oculopharyngeal muscular dystrophy (OPMD). Mutated PABPN1 proteins accumulate as insoluble intranuclear aggregates in muscles of OPMD patients. While the roles of PABPN1 in nuclear polyadenylation and regulation of alternative poly(A) site choice have been established, the molecular mechanisms which trigger pathological defects in OPMD and the role of aggregates remain to be determined. Using exon array, for the first time we have identified several splicing defects in OPMD. In particular, we have demonstrated a de...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Klein, P., Oloko, M., Roth, F., Montel, V., Malerba, A., Jarmin, S., Gidaro, T., Popplewell, L., Perie, S., Lacau St Guily, J., de la Grange, P., Antoniou, M. N., Dickson, G., Butler-Browne, G., Bastide, B., Mouly, V., Trollet, C. Tags: RNA Source Type: research
A multi-step model for facilitated unwinding of the yeast U4/U6 RNA duplex
The small nuclear RNA (snRNA) components of the spliceosome undergo many conformational rearrangements during its assembly, catalytic activation and disassembly. The U4 and U6 snRNAs are incorporated into the spliceosome as a base-paired complex within the U4/U6.U5 small nuclear ribonucleoprotein (tri-snRNP). U4 and U6 are then unwound in order for U6 to pair with U2 to form the spliceosome's active site. After splicing, U2/U6 is unwound and U6 annealed to U4 to reassemble the tri-snRNP. U6 rearrangements are crucial for spliceosome formation but are poorly understood. We have used single-molecule Förster resonance...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Rodgers, M. L., Didychuk, A. L., Butcher, S. E., Brow, D. A., Hoskins, A. A. Tags: RNA Source Type: research
Role of mRNA structure in the control of protein folding
Specific structures in mRNA modulate translation rate and thus can affect protein folding. Using the protein structures from two eukaryotes and three prokaryotes, we explore the connections between the protein compactness, inferred from solvent accessibility, and mRNA structure, inferred from mRNA folding energy (G). In both prokaryotes and eukaryotes, the G value of the most stable 30 nucleotide segment of the mRNA (Gmin) strongly, positively correlates with protein solvent accessibility. Thus, mRNAs containing exceptionally stable secondary structure elements typically encode compact proteins. The correlations between G ...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Faure, G., Ogurtsov, A. Y., Shabalina, S. A., Koonin, E. V. Tags: RNA Source Type: research
Roles for APRIN (PDS5B) in homologous recombination and in ovarian cancer prediction
APRIN (PDS5 cohesin associated factor B) interacts with both the cohesin complex and the BRCA2 tumor suppressor. How APRIN influences cohesion and DNA repair processes is not well understood. Here, we show that APRIN is recruited to DNA damage sites. We find that APRIN interacts directly with RAD51, PALB2 and BRCA2. APRIN stimulates RAD51-mediated DNA strand invasion. APRIN also binds DNA with an affinity for D-loop structures and single-strand (ss) DNA. APRIN is a new homologous recombination (HR) mediator as it counteracts the RPA inhibitory effect on RAD51 loading to ssDNA. We show that APRIN strongly improves the annea...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Couturier, A. M., Fleury, H., Patenaude, A.-M., Bentley, V. L., Rodrigue, A., Coulombe, Y., Niraj, J., Pauty, J., Berman, J. N., Dellaire, G., Di Noia, J. M., Mes-Masson, A.-M., Masson, J.-Y. Tags: Nucleic Acid Enzymes Source Type: research
RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting
Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei. In mitochondria of this pathogen, most mRNAs are internally modified by U-insertion/deletion editing while guide RNAs and rRNAs are U-tailed. The founding member of TUTase family, RNA editing TUTase 1 (RET1), functions as a subunit of the 3' processome in uridylation of gRNA precursors and mature guide RNAs. Along with KPAP1 pol...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Rajappa-Titu, L., Suematsu, T., Munoz-Tello, P., Long, M., Demir, O., Cheng, K. J., Stagno, J. R., Luecke, H., Amaro, R. E., Aphasizheva, I., Aphasizhev, R., Thore, S. Tags: Nucleic Acid Enzymes Source Type: research
Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation
The Escherichia coli type I-E CRISPR-Cas system Cascade effector is a multisubunit complex that binds CRISPR RNA (crRNA). Through its 32-nucleotide spacer sequence, Cascade-bound crRNA recognizes protospacers in foreign DNA, causing its destruction during CRISPR interference or acquisition of additional spacers in CRISPR array during primed CRISPR adaptation. Within Cascade, the crRNA spacer interacts with a hexamer of Cas7 subunits. We show that crRNAs with a spacer length reduced to 14 nucleotides cause primed adaptation, while crRNAs with spacer lengths of more than 20 nucleotides cause both primed adaptation and target...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Kuznedelov, K., Mekler, V., Lemak, S., Tokmina-Lukaszewska, M., Datsenko, K. A., Jain, I., Savitskaya, E., Mallon, J., Shmakov, S., Bothner, B., Bailey, S., Yakunin, A. F., Severinov, K., Semenova, E. Tags: Nucleic Acid Enzymes Source Type: research
Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa
Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified a tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance to oxidative stress. Analysis of tRNA from a trmJ mutant revealed that TrmJ catalyzes formation of Cm, Um, and, unexpectedly, Am. Defined in vitro analyses revealed that tRNAMet(CAU) and tRNATrp(CCA) are substrates for Cm formation, tRNAGln(UUG), tRNAPro(UGG), tRNAPro(CGG) and tRNAHis(GUG) for Um, and tRNAPro(GGG) for Am. tRNASer(UGA), previously observed...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Jaroensuk, J., Atichartpongkul, S., Chionh, Y. H., Wong, Y. H., Liew, C. W., McBee, M. E., Thongdee, N., Prestwich, E. G., DeMott, M. S., Mongkolsuk, S., Dedon, P. C., Lescar, J., Fuangthong, M. Tags: Nucleic Acid Enzymes Source Type: research
