Relevant bibliographies by topics / Dbr1p

Academic literature on the topic 'Dbr1p'

Author: Grafiati
Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Dbr1p"

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Salem, Laura A., Christopher L. Boucher, and Thomas M. Menees. "Relationship between RNA Lariat Debranching and Ty1 Element Retrotransposition." Journal of Virology 77, no. 23 (December 1, 2003): 12795–806. http://dx.doi.org/10.1128/jvi.77.23.12795-12806.2003.

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ABSTRACT The Saccharomyces cerevisiae DBR1 gene encodes a 2′-5′ phosphodiesterase that debranches intron RNA lariats following splicing. Yeast dbr1 mutants accumulate intron lariats and are also defective for mobility of the retrotransposons Ty1 and Ty3. We used a mutagenic PCR method to generate a collection of dbr1 mutant alleles to explore the relationship between the roles of DBR1 in transposition and debranching. Eight mutants defective for Ty1 transposition contained single amino acid changes in Dbr1p. Two mutations, G84A and N85D, are in a conserved phosphoesterase motif that is believed to be part of the active site of the enzyme, supporting a connection between enzymatic activity and Ty1 transposition. Two other mutations, Y68F and Y68D, occur at a potential phosphorylation site, and we have shown that Dbr1p is phosphorylated on tyrosine. We have developed an RNase protection assay to quantitate intron RNA accumulation in cells. The assay uses RNA probes that hybridize to ACT1 intron RNA. Protection patterns confirm that sequences from the 5′ end of the intron to the lariat branch point accumulate in dbr1 mutants in a branched (lariat) conformation. RNase protection assays indicate that all of the newly generated dbr1 mutant alleles are also deficient for debranching, further supporting a role for 2′-5′ phosphodiesterase activity in Ty1 transposition. A Ty1 element lacking most of its internal sequences transposes independently of DBR1. The existence of Dbr1p-dependent Ty1 sequences raises the possibility that Dbr1p acts on Ty1 RNA.
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Karst, Stephanie M., Marie-Louise Rütz, and Thomas M. Menees. "The Yeast Retrotransposons Ty1 and Ty3 Require the RNA Lariat Debranching Enzyme, Dbr1p, for Efficient Accumulation of Reverse Transcripts." Biochemical and Biophysical Research Communications 268, no. 1 (February 2000): 112–17. http://dx.doi.org/10.1006/bbrc.1999.2048.

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Menees, Thomas M. "Saccharomyces cerevisiae RNA lariat debranching enzyme, Dbr1p, is required for completion of reverse transcription by the retrovirus-like element Ty1 and cleaves branched Ty1 RNAs." Molecular Genetics and Genomics 296, no. 2 (January 19, 2021): 409–22. http://dx.doi.org/10.1007/s00438-020-01753-y.

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FABER, A. W. "The RNA catabolic enzymes Rex4p, Rnt1p, and Dbr1p show genetic interaction with trans-acting factors involved in processing of ITS1 in Saccharomyces cerevisiae pre-rRNA." RNA 10, no. 12 (December 1, 2004): 1946–56. http://dx.doi.org/10.1261/rna.7155904.

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Xu, Xiaoqin, Xin Yang, Xue Liu, Yanghui Bi, Pengzhou Kong, Yanqiang Wang, Xiaolong Cheng, and Yanfeng Xi. "The Role of DBR1 as a Candidate Prognosis Biomarker in Esophageal Squamous Cell Carcinoma." Technology in Cancer Research & Treatment 21 (January 2022): 153303382210831. http://dx.doi.org/10.1177/15330338221083105.

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Aims: Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent malignancies with unfavorable clinical outcomes and limited therapeutic methods. As a key enzyme in RNA metabolism, debranching RNA Lariats 1 (DBR1) is involved in intron turnover and biogenesis of noncoding RNA. Although cancer cells often show disorder of nucleic acid metabolism, it is unclear whether DBR1 has any effect on the carcinogenesis and progression of ESCC. Methods: Here we detected DBR1 expression in 112 ESCC samples by immunohistochemistry and analyzed its correlation with clinical parameters and survival. Results: DBR1 is mainly located in the nucleus of ESCC tissue. And DBR1 was associated with several malignant clinical features in patients, including tumor location ( χ2 = 9.687, P = .021), pathologic T stage ( χ2 = 5.771, P = .016), lymph node metastasis ( χ2 = 8.215, P = .004) and N classification ( χ2 = 10.066, P = .018). Moreover, Kaplan-Meier analysis showed that ESCC patients harboring lower DBR1 expression had a worse prognosis in comparison with those with higher DBR1 expression ( P = .005). Univariate and multivariate Cox proportional hazards regression analyses indicated that decreased DBR1 might act as an independent predictor of poor prognosis for ESCC patients. Conclusion: Abnormal RNA metabolism might play a critical role in promoting the progression of ESCC, and DBR1 may be a promising potential biomarker for predicting the prognosis of ESCC patients.
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Chen, G. C., L. Zheng, and C. S. Chan. "The LIM domain-containing Dbm1 GTPase-activating protein is required for normal cellular morphogenesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 16, no. 4 (April 1996): 1376–90. http://dx.doi.org/10.1128/mcb.16.4.1376.

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Normal cell growth in the yeast Saccharomyces cerevisiae involves the selection of genetically determined bud sites where most growth is localized. Previous studies have shown that BEM2, which encodes a GTPase-activating protein (GAP) that is specific for the Rho-type GTPase Rho1p in vitro, is required for proper bud site selection and bud emergence. We show here that DBM1, which encodes another putative Rho-type GAP with two tandemly arranged cysteine-rich LIM domains, also is needed for proper bud site selection, as haploid cells lacking Dbm1p bud predominantly in a bipolar, rather than the normal axial, manner. Furthermore, yeast cells lacking both Bem2p and Dbm1p are inviable. The nonaxial budding defect of dbm1 mutants can be rescued partially by overproduction of Bem3p and is exacerbated by its absence. Since Bem3p has previously been shown to function as a GAP for Cdc42p, and also less efficiently for Rho1p, our results suggest that Dbm1p, like Bem2p and Bem3p, may function in vivo as a GAP for Cdc42p and/or Rho1p. Both LIM domains of Dbm1p are essential for its normal function. Point mutations that alter single conserved cysteine residues within either LIM domain result in mutant forms of Dbm1p that can no longer function in bud site selection but instead are capable of rescuing the inviability of bem2 mutants at 35 degrees C.
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Clark, Nathaniel E., Adam Katolik, Kenneth M. Roberts, Alexander B. Taylor, Stephen P. Holloway, Jonathan P. Schuermann, Eric J. Montemayor, et al. "Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1." Proceedings of the National Academy of Sciences 113, no. 51 (December 6, 2016): 14727–32. http://dx.doi.org/10.1073/pnas.1612729114.

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Intron lariats are circular, branched RNAs (bRNAs) produced during pre-mRNA splicing. Their unusual chemical and topological properties arise from branch-point nucleotides harboring vicinal 2′,5′- and 3′,5′-phosphodiester linkages. The 2′,5′-bonds must be hydrolyzed by the RNA debranching enzyme Dbr1 before spliced introns can be degraded or processed into small nucleolar RNA and microRNA derived from intronic RNA. Here, we measure the activity of Dbr1 fromEntamoeba histolyticaby using a synthetic, dark-quenched bRNA substrate that fluoresces upon hydrolysis. Purified enzyme contains nearly stoichiometric equivalents of Fe and Zn per polypeptide and demonstrates turnover rates of ∼3 s−1. Similar rates are observed when apo-Dbr1 is reconstituted with Fe(II)+Zn(II) under aerobic conditions. Under anaerobic conditions, a rate of ∼4.0 s−1is observed when apoenzyme is reconstituted with Fe(II). In contrast, apo-Dbr1 reconstituted with Mn(II) or Fe(II) under aerobic conditions is inactive. Diffraction data from crystals of purified enzyme using X-rays tuned to the Fe absorption edge show Fe partitions primarily to the β-pocket and Zn to the α-pocket. Structures of the catalytic mutant H91A in complex with 7-mer and 16-mer synthetic bRNAs reveal bona fide RNA branchpoints in the Dbr1 active site. A bridging hydroxide is in optimal position for nucleophilic attack of the scissile phosphate. The results clarify uncertainties regarding structure/function relationships in Dbr1 enzymes, and the fluorogenic probe permits high-throughput screening for inhibitors that may hold promise as treatments for retroviral infections and neurodegenerative disease.
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Nam, K., G. Lee, J. Trambley, S. E. Devine, and J. D. Boeke. "Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation." Molecular and Cellular Biology 17, no. 2 (February 1997): 809–18. http://dx.doi.org/10.1128/mcb.17.2.809.

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The cDNAs and genes encoding the intron lariat-debranching enzyme were isolated from the nematode Caenorhabditis elegans and the fission yeast Schizosaccharomyces pombe based on their homology with the Saccharomyces cerevisiae gene. The cDNAs were shown to be functional in an interspecific complementation experiment; they can complement an S. cerevisiae dbr1 null mutant. About 2.5% of budding yeast S. cerevisiae genes have introns, and the accumulation of excised introns in a dbr1 null mutant has little effect on cell growth. In contrast, many S. pombe genes contain introns, and often multiple introns per gene, so that S. pombe is estimated to contain approximately 40 times as many introns as S. cerevisiae. The S. pombe dbr1 gene was disrupted and shown to be nonessential. Like the S. cerevisiae mutant, the S. pombe null mutant accumulated introns to high levels, indicating that intron lariat debranching represents a rate-limiting step in intron degradation in both species. Unlike the S. cerevisiae mutant, the S. pombe dbr1::leu1+ mutant had a severe growth defect and exhibited an aberrant elongated cell shape in addition to an intron accumulation phenotype. The growth defect of the S. pombe dbr1::leu1+ strain suggests that debranching activity is critical for efficient intron RNA degradation and that blocking this pathway interferes with cell growth.
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Utkin, I., D. D. Dalton, and J. Wiegel. "Specificity of Reductive Dehalogenation of Substituted ortho-Chlorophenols by Desulfitobacterium dehalogenans JW/IU-DC1." Applied and Environmental Microbiology 61, no. 4 (April 1995): 1677. http://dx.doi.org/10.1128/aem.61.4.1677-1677c.1995.

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Volume 61, no. 1, abstract, lines 4 and 5: "2,6-dichloro-4-R-phenols, where . . ." should read "2,6-dichloro-4-R-phenols (2,6-DCl-4-RPs, where R is -H, -F, -Cl, -NO(inf2), -CO(inf2)(sup-), or -COOCH(inf3)) . . ." Line 6: ". . . bromophenols (2-BrP, 2,6-DBrP, and 2-Br-4ClP)" should read ". . . the bromophenols 2-BrP, 2,6-DBrP, and 2-Br-4-ClP." [This corrects the article on p. 346 in vol. 61.].
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Zhang, Yansheng, Keat H. Teoh, Darwin W. Reed, and Patrick S. Covello. "Molecular cloning and characterization of Dbr1, a 2-alkenal reductase from Artemisia annuaThe nucleotide sequence reported in this article has been deposited in the GenBank database under accession No. FJ750460.This paper is one of a selection of papers published in a Special Issue from the National Research Council of Canada – Plant Biotechnology Institute." Botany 87, no. 6 (June 2009): 643–49. http://dx.doi.org/10.1139/b09-033.

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The molecular genetics of carbon–carbon double bond reduction in the plant Artemisia annua L. was studied. Expressed sequence tags from this plant were investigated for sequences with similarity to known double-bond reductases. This resulted in the isolation of a cDNA, corresponding to the gene A. annua Dbr1 (Double bond reductase1), encoding a member of the medium chain dehydrogenase/reductase protein superfamily with sequence similarity to tobacco allyl alcohol dehydrogenase. Recombinant A. annua Dbr1 protein was purified from Escherischia coli and shown to catalyze the reduction of the carbon–carbon double bond of 2-alkenals. This activity included the reduction of the double bond at C11–C13 in the artemisinin precursor artemisinic aldehyde, albeit with unnatural stereochemistry. The substrate specificity, product stereochemistry, and expression pattern of A. annua Dbr1 point to its involvement in planta in the detoxification of 2-alkenals, which may be generated under oxidative stress conditions.
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Dissertations / Theses on the topic "Dbr1p"

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Hett, Anne. "Studies on the metabolism of retained and excised introns in human cells." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/10515.

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In eukaryotes the coding regions of most genes are interrupted by introns that must be removed by splicing to form a coding mRNA. However, while the splicing mechanism has received a lot of attention, much less is known about the metabolism of introns. This is partly due to the difficulties in studying introns as both aberrantly spliced transcripts and spliced introns are rapidly degraded. In this study, I have analysed intron metabolism in two respects: first I have investigated how introns are degraded following the completion of splicing. Second, I investigate the fate of transcripts, in which introns are retained due to splicing failure. In order to study the degradation of introns following splicing, I performed siRNA mediated knock down of the debrancing enzyme (Dbr1). Following splicing, introns are present in a circular lariat structure and Dbr1 is the enzyme thought to be responsible for opening this. Indeed, I found that knockdown of Dbr1 increased the amount of stabilised introns. Interestingly, introns were found to be stabilised in the cytoplasm and not in the nucleus as expected, even though immunofluoresence showed that Dbr1 is clearly nuclear. However, western blot analysis localised Dbr1 in the cytoplasm. Further investigation showed widely used methods to separate nuclear and cytoplasmic fractions are prone to generating artefacts which result in nucleoplasmic proteins delocalised to the cytoplasm. This finding may prevent future misinterpretation of data obtained by these methods. To investigate splicing failure, it was necessary to generated a sufficiently large pool of unspliced transcripts. To do this I used antisense morpholinos (AMOs) that bind to specific snRNAs (small nuclear RNAs). They are designed to block interaction surfaces that are important for splicing. Using this approach, I investigated the localisation of RNA transcripts and selected RNA processing and degradation factors in normal conditions and where splicing was inhibited. When splicing is inhibited I found splicing factors and unspliced, polyadenylated RNA localising to nuclear, splicing speckle marker SC35 positive speckles. I further discovered that for RNA to localise to nuclear speckles, polyadenylation and RNA cleavage are essential, indicating that SC-35 speckles might sequester unspliced transcripts preventing translation of potentially harmful transcripts. These transcripts remain functional however, and can be spliced where functional spliceosomes can be assembled.
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Books on the topic "Dbr1p"

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Cutting, E. J. ’Ted’. CUTTING EDGE CONVERSATIONS: The Aston Martin Race Car Chief Design/Engineer from 1949 - 1964. England: Self Published, 2012.

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Montana. Public Employees' Retirement Board., ed. Montana, the choice is yours, the time is now!: The power to control your future : DBRP Defined Benefit Retirement Plan, DCRP Defined Contribution Retirement Plan. [Helena, MT: Montana Public Employee Retirement Administration, 2007.

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Montana, the choice is yours, the time is now! workbook: The power to control your future : DBRP Defined Benefit Retirement Plan, DCRP Defined Contribution Retirement Plan. Troy, Mich: Educational Technologies, 2002.

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Book chapters on the topic "Dbr1p"

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Krupalin, Vijjeswarapu Abishek Heyer, Manapragada Lakshmi Sowmya, and Madugula Manoj Kumar. "Intelligent Computing Method for Detecting Diabetic Retinopathy (DBRP)." In Innovations in Computer Science and Engineering, 545–52. Singapore: Springer Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-8987-1_58.

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Conference papers on the topic "Dbr1p"

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Iranmanesh, Saeid, Raad Raad, and Kwan-Wu Chin. "A novel destination-based routing protocol (DBRP) in DTNs." In 2012 International Symposium on Communications and Information Technologies (ISCIT). IEEE, 2012. http://dx.doi.org/10.1109/iscit.2012.6380915.

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Yu, Haoyu, and Min Fu. "DbRMP: Predicting Douban Rating of Movies with high-dimensional Features by Comprehensive Machine Learning Algorithms." In 2022 IEEE International Conference on Artificial Intelligence and Computer Applications (ICAICA). IEEE, 2022. http://dx.doi.org/10.1109/icaica54878.2022.9844633.

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Paradowska-Gorycka, A., B. Stypinska, E. Haladyj, K. Romanowska-Prochnicka, A. Pawlik, and M. Olesinska. "THU0012 HLA-DBR1 alleles profile in patients with rheumatoid arthritis: relation to disease susceptibility and severity." In Annual European Congress of Rheumatology, 14–17 June, 2017. BMJ Publishing Group Ltd and European League Against Rheumatism, 2017. http://dx.doi.org/10.1136/annrheumdis-2017-eular.5794.

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