Journal articles: 'Transcription and translation'

1

Belczyk-Kohl, Yvonne. "Some remarks on transcript translation in discourse analysis." European Journal of Applied Linguistics 4, no. 1 (March 1, 2016): 139–64. http://dx.doi.org/10.1515/eujal-2015-0031.

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AbstractTranscripts of second language interaction and within publications in languages differing from the data discussed often must be translated to make the results of discourse analysis accessible. Transcription follows strict rules to achieve a scientific standard recipients can rely upon. Its main task is to picture a piece of authentic interaction by means of writing as detailed as possible and necessary, to make readers able to follow an analysis and judge it by themselves.But what is true for transcriptions does not hold for their translations. Surprisingly, reflection of transcript translation tends to be neglected in literature. This might be due to several reasons: the different language systems and cultural imaging habits make it difficult, if not impossible, to propose an all-fitting translation guideline for transcription. Further, discourse analysts usually are (experienced) non-professional translators and do not often have a theoretical translation background. It is an additional (practical) challenge to align the demands of transcript theory and readability with editorial requirements.While translating transcripts analysts would have to reflect five different aspects: (1) the status of translation in transcription, (2) a (not yet established) standard for transcript translation, (3) the translation‘s readability (recipients should be able to follow it with only little effort), (4) the potentially extremely differing systems of source and target language (representation of syntax and semantics), and (5) translation problems (e.g. cultural aspects) with regard to the given language pair.The article considers the status of translation in transcription. The few theoretical findings are analyzed and contrasted with examples from discourse analysis. The article is complemented with the results of a survey among analysts concerning their translation behavior. Finally, some proposals for solutions are outlined.

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Sperber, Matthias, Hendra Setiawan, Christian Gollan, Udhyakumar Nallasamy, and Matthias Paulik. "Consistent Transcription and Translation of Speech." Transactions of the Association for Computational Linguistics 8 (November 2020): 695–709. http://dx.doi.org/10.1162/tacl_a_00340.

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The conventional paradigm in speech translation starts with a speech recognition step to generate transcripts, followed by a translation step with the automatic transcripts as input. To address various shortcomings of this paradigm, recent work explores end-to-end trainable direct models that translate without transcribing. However, transcripts can be an indispensable output in practical applications, which often display transcripts alongside the translations to users. We make this common requirement explicit and explore the task of jointly transcribing and translating speech. Although high accuracy of transcript and translation are crucial, even highly accurate systems can suffer from inconsistencies between both outputs that degrade the user experience. We introduce a methodology to evaluate consistency and compare several modeling approaches, including the traditional cascaded approach and end-to-end models. We find that direct models are poorly suited to the joint transcription/translation task, but that end-to-end models that feature a coupled inference procedure are able to achieve strong consistency. We further introduce simple techniques for directly optimizing for consistency, and analyze the resulting trade-offs between consistency, transcription accuracy, and translation accuracy. 1

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Chatterjee, Surajit, Adrien Chauvier, Shiba S. Dandpat, Irina Artsimovitch, and Nils G. Walter. "A translational riboswitch coordinates nascent transcription–translation coupling." Proceedings of the National Academy of Sciences 118, no. 16 (April 13, 2021): e2023426118. http://dx.doi.org/10.1073/pnas.2023426118.

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Bacterial messenger RNA (mRNA) synthesis by RNA polymerase (RNAP) and first-round translation by the ribosome are often coupled to regulate gene expression, yet how coupling is established and maintained is ill understood. Here, we develop biochemical and single-molecule fluorescence approaches to probe the dynamics of RNAP–ribosome interactions on an mRNA with a translational preQ1-sensing riboswitch in its 5′ untranslated region. Binding of preQ1 leads to the occlusion of the ribosome binding site (RBS), inhibiting translation initiation. We demonstrate that RNAP poised within the mRNA leader region promotes ribosomal 30S subunit binding, antagonizing preQ1-induced RBS occlusion, and that the RNAP–30S bridging transcription factors NusG and RfaH distinctly enhance 30S recruitment and retention, respectively. We further find that, while 30S–mRNA interaction significantly impedes RNAP in the absence of translation, an actively translating ribosome promotes productive transcription. A model emerges wherein mRNA structure and transcription factors coordinate to dynamically modulate the efficiency of transcription–translation coupling.

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Penno, Christophe, and Claude Parsot. "Transcriptional Slippage in mxiE Controls Transcription and Translation of the Downstream mxiD Gene, Which Encodes a Component of the Shigella flexneri Type III Secretion Apparatus." Journal of Bacteriology 188, no. 3 (February 1, 2006): 1196–98. http://dx.doi.org/10.1128/jb.188.3.1196-1198.2006.

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ABSTRACT The Shigella flexneri transcription activator MxiE is produced by transcriptional slippage from two overlapping open reading frames. By using plasmids encoding a mxiD-lacZ translational fusion, we showed that transcriptional slippage in mxiE influences both transcription and translation of the downstream mxiD gene encoding an essential component of the type III secretion apparatus.

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5

Vinson, Valda. "Coupling transcription and translation." Science 356, no. 6334 (April 13, 2017): 149.17–151. http://dx.doi.org/10.1126/science.356.6334.149-q.

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Kimberling, William J. "Transcription, Translation, and Transitions." Audiology and Neurotology 9, no. 1 (December 19, 2003): 1. http://dx.doi.org/10.1159/000074182.

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Vinson, Valda. "Coupling transcription and translation." Science 369, no. 6509 (September 10, 2020): 1335.2–1335. http://dx.doi.org/10.1126/science.369.6509.1335-b.

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8

Pislaru, Sorin, and Robert D. Simari. "The Translation of Transcription." Circulation Research 97, no. 11 (November 25, 2005): 1083–84. http://dx.doi.org/10.1161/01.res.0000194573.70503.b9.

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9

Wang, Chengyuan, Vadim Molodtsov, Emre Firlar, Jason T. Kaelber, Gregor Blaha, Min Su, and Richard H. Ebright. "Structural basis of transcription-translation coupling." Science 369, no. 6509 (August 20, 2020): 1359–65. http://dx.doi.org/10.1126/science.abb5317.

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In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)–synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ribosome-translating mRNA. Coupling is modulated by the transcription factors NusG (which is thought to bridge RNAP and the ribosome) and NusA. Here, we report cryo–electron microscopy structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A, previously termed “expressome”). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.

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10

Stevenson-Jones, Flint, Jason Woodgate, Daniel Castro-Roa, and Nikolay Zenkin. "Ribosome reactivates transcription by physically pushing RNA polymerase out of transcription arrest." Proceedings of the National Academy of Sciences 117, no. 15 (April 1, 2020): 8462–67. http://dx.doi.org/10.1073/pnas.1919985117.

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In bacteria, the first two steps of gene expression—transcription and translation—are spatially and temporally coupled. Uncoupling may lead to the arrest of transcription through RNA polymerase backtracking, which interferes with replication forks, leading to DNA double-stranded breaks and genomic instability. How transcription–translation coupling mitigates these conflicts is unknown. Here we show that, unlike replication, translation is not inhibited by arrested transcription elongation complexes. Instead, the translating ribosome actively pushes RNA polymerase out of the backtracked state, thereby reactivating transcription. We show that the distance between the two machineries upon their contact on mRNA is smaller than previously thought, suggesting intimate interactions between them. However, this does not lead to the formation of a stable functional complex between the enzymes, as was once proposed. Our results reveal an active, energy-driven mechanism that reactivates backtracked elongation complexes and thus helps suppress their interference with replication.

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Gong, Feng, and Charles Yanofsky. "A Transcriptional Pause Synchronizes Translation with Transcription in the Tryptophanase Operon Leader Region." Journal of Bacteriology 185, no. 21 (November 1, 2003): 6472–76. http://dx.doi.org/10.1128/jb.185.21.6472-6476.2003.

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ABSTRACT Regulation of transcription of the tryptophanase operon requires that translation of its leader peptide coding region, tnaC, be coupled with its transcription. We show in vitro that a transcription pause site exists at the end of the tnaC coding region and that translation of tnaC releases the paused transcription complex, coupling transcription with translation.

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Schmeidler-Sapiro, K. T., T. R. Johnson, J. Ilan, and J. Ilan. "Regulation of transcription by translational components in coupled translation-transcription cell-free system." Biochimie 74, no. 5 (May 1992): 495–510. http://dx.doi.org/10.1016/0300-9084(92)90091-r.

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13

Hudson, D., and R. Edwards. "Dynamics of transcription–translation networks." Physica D: Nonlinear Phenomena 331 (September 2016): 102–13. http://dx.doi.org/10.1016/j.physd.2016.05.013.

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Stern, David S., David C. Higgs, and Jianjun Yang. "Transcription and translation in chloroplasts." Trends in Plant Science 2, no. 8 (August 1997): 308–15. http://dx.doi.org/10.1016/s1360-1385(97)89953-0.

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15

D’Souza, Aaron R., and Michal Minczuk. "Mitochondrial transcription and translation: overview." Essays in Biochemistry 62, no. 3 (July 20, 2018): 309–20. http://dx.doi.org/10.1042/ebc20170102.

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Mitochondria are the major source of ATP in the cell. Five multi-subunit complexes in the inner membrane of the organelle are involved in the oxidative phosphorylation required for ATP production. Thirteen subunits of these complexes are encoded by the mitochondrial genome often referred to as mtDNA. For this reason, the expression of mtDNA is vital for the assembly and functioning of the oxidative phosphorylation complexes. Defects of the mechanisms regulating mtDNA gene expression have been associated with deficiencies in assembly of these complexes, resulting in mitochondrial diseases. Recently, numerous factors involved in these processes have been identified and characterized leading to a deeper understanding of the mechanisms that underlie mitochondrial diseases.

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16

Pentimalli, Francesca. "Transcription and translation get together." Nature Reviews Genetics 8, no. 3 (February 6, 2007): 168. http://dx.doi.org/10.1038/nrg2069.

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Swami, Meera. "Directly linking transcription and translation." Nature Reviews Genetics 11, no. 6 (May 11, 2010): 389. http://dx.doi.org/10.1038/nrg2803.

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Fu, Jingjing, Yunkun Dang, Christopher Counter, and Yi Liu. "Codon usage regulates human KRAS expression at both transcriptional and translational levels." Journal of Biological Chemistry 293, no. 46 (October 1, 2018): 17929–40. http://dx.doi.org/10.1074/jbc.ra118.004908.

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KRAS and HRAS are highly homologous oncogenic Ras GTPase family members that are mutated in a wide spectrum of human cancers. Despite having high amino acid identity, KRAS and HRAS have very different codon usage biases: the HRAS gene contains many common codons, and KRAS is enriched for rare codons. Rare codons in KRAS suppress its protein expression, which has been shown to affect both normal and cancer biology in mammals. Here, using HRAS or KRAS expression in different human cell lines and in vitro transcription and translation assays, we show that KRAS rare codons inhibit both translation efficiency and transcription and that the contribution of these two processes varies among different cell lines. We observed that codon usage regulates mRNA translation efficiency such that WT KRAS mRNA is poorly translated. On the other hand, common codons increased transcriptional rates by promoting activating histone modifications and recruitment of transcriptional coactivators. Finally, we found that codon usage also influences KRAS protein conformation, likely because of its effect on co-translational protein folding. Together, our results reveal that codon usage has multidimensional effects on protein expression, ranging from effects on transcription to protein folding in human cells.

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Lukachevskaja, Lilianna А., and Irina V. Sobakina. "Translation of the culture-specific vocabulary in the Yakut heroic epic olonkho into Russian and English (based on the material of olonkho “Nurgun Bootur the Swift” by P.A. Oyunsky)." Philological Sciences. Scientific Essays of Higher Education, no. 4 (July 2021): 18–26. http://dx.doi.org/10.20339/phs.4-21.018.

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The culture-specific vocabulary in the texts of epic works, which expresses the peculiarity of the culture of the people, creates certain difficulties in translation. In the proposed study, the analysis of the transmission of culture-specific vocabulary Olonkho “Nurgun Bootur the Swift” by P.A. Sleptsova in Russian and English. 825 examples were collected and grouped based on the classification of S. Vlakhov and S. Florin, the following groups were identified: proper names, realities, phraseological units, addresses, interjections, onomatopoeia. The analysis of the translation revealed that the most commonly used methods are transcription when translating proper names, realities and interjections; descriptive translation when translating proper names and realities as a commentary to the text, as well as, in some cases, when translating realities, phraseological units and addresses is used in the text itself; approximate translation when translating addresses, phraseological units and onomatopoeia. In the translations under consideration, the national flavor and specificity of the original language are preserved, and the translation methods are used in approximately the same amount for each group of of culture-specific vocabulary.

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Veenstra, Gert Jan C., Olivier H. J. Destrée, and Alan P. Wolffe. "Translation of Maternal TATA-Binding Protein mRNA Potentiates Basal but Not Activated Transcription in Xenopus Embryos at the Midblastula Transition." Molecular and Cellular Biology 19, no. 12 (December 1, 1999): 7972–82. http://dx.doi.org/10.1128/mcb.19.12.7972.

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ABSTRACT Early embryonic development in Xenopus laevis is characterized by transcriptional repression which is relieved at the midblastula stage (MBT). Here we show that the relative abundance of TATA-binding protein (TBP) increases robustly at the MBT and that the mechanism underlying this increase is translation of maternally stored TBP RNA. We show that TBP is rate-limiting in egg extract under conditions that titrate nucleosome assembly. Precocious translation of TBP mRNA in Xenopus embryos facilitates transcription before the MBT, without requiring TBP to be prebound to the promoter before injection. This effect is transient in the absence of chromatin titration and is sustained when chromatin is titrated. These data show that translational regulation of TBP RNA contributes to limitations on the transcriptional capacity before the MBT. Second, we examined the ability of trans-acting factors to contribute to promoter activity before the MBT. Deletion of cis-acting elements does not affect histone H2B transcription in egg extract, a finding indicative of limited trans-activation. Moreover, in the context of the intact promoter, neither the transcriptional activator Oct-1, nor TBP, nor TFIID enable transcriptional activation in vitro. HeLa cell extract, however, reconstitutes activated transcription in mixed extracts. These data suggest a deficiency in egg extract cofactors required for activated transcription. We show that the capacity for activated H2B transcription is gradually acquired at the early gastrula transition. This transition occurs well after the blastula stage when the basal transcription machinery can first be complemented with TBP.

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Wiese, A., N. Elzinga, B. Wobbes, and S. Smeekens. "Sucrose-induced translational repression of plant bZIP-type transcription factors." Biochemical Society Transactions 33, no. 1 (February 1, 2005): 272–75. http://dx.doi.org/10.1042/bst0330272.

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Sugars as signalling molecules exert control on the transcription of many plant genes. Sugar signals also alter mRNA and protein stability. Increased sucrose concentrations specifically repress translation of the S-class basic region leucine zipper (bZIP) type transcription factor AtbZIP11/ATB2. This sucrose-induced repression of translation (SIRT) depends on translation of a highly conserved upstream open reading frame (uORF) in the 5′ UTR of the gene. This conserved uORF is exclusively encoded in 5′ UTRs of several plant S-class bZIP transcription factors. Arabidopsis homologues of ATB2/AtbZIP11, which harbour the conserved uORF, also show SIRT. Therefore, SIRT emerges as a general sucrose translational control mechanism of a group of transcription factors. SIRT might be part of a sucrose-specific signalling pathway, controlling expression of plant bZIP transcription factor genes.

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Xie, Jianling, Eric P. Kusnadi, Luc Furic, and Luke A. Selth. "Regulation of mRNA Translation by Hormone Receptors in Breast and Prostate Cancer." Cancers 13, no. 13 (June 29, 2021): 3254. http://dx.doi.org/10.3390/cancers13133254.

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Breast and prostate cancer are the second and third leading causes of death amongst all cancer types, respectively. Pathogenesis of these malignancies is characterised by dysregulation of sex hormone signalling pathways, mediated by the estrogen receptor-α (ER) in breast cancer and androgen receptor (AR) in prostate cancer. ER and AR are transcription factors whose aberrant function drives oncogenic transcriptional programs to promote cancer growth and progression. While ER/AR are known to stimulate cell growth and survival by modulating gene transcription, emerging findings indicate that their effects in neoplasia are also mediated by dysregulation of protein synthesis (i.e., mRNA translation). This suggests that ER/AR can coordinately perturb both transcriptional and translational programs, resulting in the establishment of proteomes that promote malignancy. In this review, we will discuss relatively understudied aspects of ER and AR activity in regulating protein synthesis as well as the potential of targeting mRNA translation in breast and prostate cancer.

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Gorchakov, Rodion, Elena Frolova, and Ilya Frolov. "Inhibition of Transcription and Translation in Sindbis Virus-Infected Cells." Journal of Virology 79, no. 15 (August 1, 2005): 9397–409. http://dx.doi.org/10.1128/jvi.79.15.9397-9409.2005.

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ABSTRACT Alphaviruses are arthropod-borne viruses (arboviruses) that include a number of important human and animal pathogens. The natural transmission cycle of alphaviruses requires their presence at high concentrations in the blood of amplification hosts for efficient infection of mosquito vectors. The high-titer viremia development implies multiple rounds of infection that proceed in the background of the developing antiviral cell response aimed at blocking virus spread on an organismal level. Therefore, as for many viruses, if not most of them, alphaviruses have evolved mechanisms directed toward downregulating different components of the antiviral cell reaction and increasing viremia to a level sufficient for the next round of transmission. Using Sindbis virus (SIN) as a model, we demonstrated that (i) the replication of wild-type SIN strongly affects major cellular processes, e.g., transcription and translation of mRNAs; (ii) transcriptional and translational shutoffs are distinctly independent events, and their development can be differentially manipulated by creating different mutations in SIN nonstructural protein nsP2; and (iii) inhibition of transcription, but not translation, is a critical mechanism that SIN employs to suppress the expression of cellular viral stress-inducible genes in cells of vertebrate origin. Downregulation of transcription of all of the cellular mRNAs appears to be a very efficient means of reducing the development of an antiviral response. The ability to cause transcriptional shutoff may partially determine SIN host range and replication in particular tissues.

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Hu, Wenqian, Bingbing Yuan, and Harvey F. Lodish. "Cpeb4-Mediated Translational Regulatory Circuitry Controls Terminal Erythroid Differentiation." Blood 124, no. 21 (December 6, 2014): 4012. http://dx.doi.org/10.1182/blood.v124.21.4012.4012.

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Abstract While we have considerable understanding of the transcriptional networks controlling mammalian cell differentiation, our knowledge of post-transcriptional regulatory events is very limited. Using differentiation of primary erythroid cells as a model, we show that the sequence-specific mRNA-binding protein Cpeb4 is induced by the erythroid important transcription factors Gata1 and Tal1, is strongly upregulated during terminal erythroid development, and is essential for terminal erythropoiesis. By binding directly to the translation initiation factor eIF3 complex, Cpeb4 represses the translation of a large set of mRNAs, most of which are normally downregulated during terminal erythroid development. Cpeb4 also binds to its own mRNA to repress its translation, and ectopic expression of Cpeb4 blocks erythroid differentiation. Thus transcriptional induction and translational repression combine to form a negative feedback loop to control Cpeb4 protein levels within a specific range that is required for terminal erythropoiesis. Our study provides an example of how translational control is integrated with transcriptional regulation to precisely control gene expression during mammalian cell differentiation. Disclosures No relevant conflicts of interest to declare.

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Aldridge, Phillip, Joshua Gnerer, Joyce E. Karlinsey, and Kelly T. Hughes. "Transcriptional and Translational Control of the Salmonella fliC Gene." Journal of Bacteriology 188, no. 12 (June 15, 2006): 4487–96. http://dx.doi.org/10.1128/jb.00094-06.

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ABSTRACT The flagellin gene fliC encodes the major component of the flagellum in Salmonella enterica serovar Typhimurium. This study reports the identification of a signal within the 5′ untranslated region (5′UTR) of the fliC transcript required for the efficient expression and assembly of FliC into the growing flagellar structure. Primer extension mapping determined the transcription start site of the fliC flagellin gene to be 62 bases upstream of the AUG start codon. Using tetA-fliC operon fusions, we show that the entire 62-base 5′UTR region of fliC was required for sufficient fliC mRNA translation to allow normal FliC flagellin assembly, suggesting that translation might be coupled to assembly. To identify sequence that might couple fliC mRNA translation to FliC secretion, the 5′ end of the chromosomal fliC gene was mutagenized by PCR-directed mutagenesis. Single base sequences important for fliC-dependent transcription, translation, and motility were identified by using fliC-lacZ transcriptional and translational reporter constructs. Transcription-specific mutants identified the −10 and −35 regions of the consensus flagellar class 3 gene promoter. Single base changes defective in translation were located in three regions: the AUG start codon, the presumed ribosomal binding site region, and a region near the very 5′ end of the fliC mRNA that corresponded to a potential stem-loop structure in the 5′UTR. Motility-specific mutants resulted from base substitutions only in the fliC-coding region. The results suggest that fliC mRNA translation is not coupled to FliC secretion by the flagellar type III secretion system.

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O’Reilly, Francis J., Liang Xue, Andrea Graziadei, Ludwig Sinn, Swantje Lenz, Dimitry Tegunov, Cedric Blötz, et al. "In-cell architecture of an actively transcribing-translating expressome." Science 369, no. 6503 (July 30, 2020): 554–57. http://dx.doi.org/10.1126/science.abb3758.

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Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae. We combined whole-cell cross-linking mass spectrometry, cellular cryo–electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at subnanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA at the interface between a NusG-bound elongating RNAP and the ribosome and propose that it can mediate transcription-translation coupling. Translation inhibition dissociated the expressome, whereas transcription inhibition stalled and rearranged it. Thus, the active expressome architecture requires both translation and transcription elongation within the cell.

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Steffensen, Lotte, and Per Amstrup Pedersen. "Heterologous Expression of Membrane and Soluble Proteins Derepresses GCN4 mRNA Translation in the Yeast Saccharomyces cerevisiae." Eukaryotic Cell 5, no. 2 (February 2006): 248–61. http://dx.doi.org/10.1128/ec.5.2.248-261.2006.

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ABSTRACT This paper describes the first physiological response at the translational level towards heterologous protein production in Saccharomyces cerevisiae. In yeast, the phosphorylation of eukaryotic initiation factor 2α (eIF-2α) by Gcn2p protein kinase mediates derepression of GCN4 mRNA translation. Gcn4p is a transcription factor initially found to be required for transcriptional induction of genes responsible for amino acid or purine biosynthesis. Using various GCN4-lacZ fusions, knockout yeast strains, and anti-eIF-2α-P/anti-eIF-2α antibodies, we observed that heterologous expression of the membrane-bound α1β1 Na,K-ATPase from pig kidney, the rat pituitary adenylate cyclase seven-transmembrane-domain receptor, or a 401-residue soluble part of the Na,K-ATPase α1 subunit derepressed GCN4 mRNA translation up to 70-fold. GCN4 translation was very sensitive to the presence of heterologous protein, as a density of 1‰ of heterologous membrane protein derepressed translation maximally. Translational derepression of GCN4 was not triggered by misfolding in the endoplasmic reticulum, as expression of the wild type or temperature-sensitive folding mutants of the Na,K-ATPase increased GCN4 translation to the same extent. In situ activity of the heterologously expressed protein was not required for derepression of GCN4 mRNA translation, as illustrated by the expression of an enzymatically inactive Na,K-ATPase. Two- to threefold overexpression of the highly abundant and plasma membrane-located endogenous H-ATPase also induced GCN4 translation. Derepression of GCN4 translation required phosphorylation of eIF-2α, the tRNA binding domain of Gcn2p, and the ribosome-associated proteins Gcn1p and Gcn20p. The increase in Gcn4p density in response to heterologous expression did not induce transcription from the HIS4 promoter, a traditional Gcn4p target.

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Thomann, J. "The Name Picatrix: Transcription or Translation?" Journal of the Warburg and Courtauld Institutes 53 (1990): 289. http://dx.doi.org/10.2307/751354.

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Sossin, Wayne S. "“Fragile” equilibrium between translation and transcription." Proceedings of the National Academy of Sciences 115, no. 48 (November 14, 2018): 12086–88. http://dx.doi.org/10.1073/pnas.1817562115.

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Dong, Zigang, and Ann M. Bode. "Proceedings—targeting carcinogenesis: Transduction, transcription, translation." Molecular Carcinogenesis 45, no. 6 (2006): 353–54. http://dx.doi.org/10.1002/mc.20227.

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Peattie, Matthew. "Chant notation in transcription and translation." Early Music 44, no. 1 (February 2016): 125–40. http://dx.doi.org/10.1093/em/caw014.

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An, W., and J. W. Chin. "Synthesis of orthogonal transcription-translation networks." Proceedings of the National Academy of Sciences 106, no. 21 (May 14, 2009): 8477–82. http://dx.doi.org/10.1073/pnas.0900267106.

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Bader, Andreas G., Sohye Kang, Li Zhao, and Peter K. Vogt. "Oncogenic PI3K deregulates transcription and translation." Nature Reviews Cancer 5, no. 12 (December 2005): 921–29. http://dx.doi.org/10.1038/nrc1753.

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Garber, Kathryn, Karen T. Smith, Danny Reines, and Stephen T. Warren. "Transcription, translation and fragile X syndrome." Current Opinion in Genetics & Development 16, no. 3 (June 2006): 270–75. http://dx.doi.org/10.1016/j.gde.2006.04.010.

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Shu, Yuan, and Lin Hong-Hui. "Transcription, translation, degradation, and circadian clock." Biochemical and Biophysical Research Communications 321, no. 1 (August 2004): 1–6. http://dx.doi.org/10.1016/j.bbrc.2004.06.093.

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Patrick, GA. "Transcription and Translation — A Practical Approach." Biochemical Education 13, no. 2 (April 1985): 93. http://dx.doi.org/10.1016/0307-4412(85)90051-2.

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Nollet, Kenneth E. "Lost in Transcription, Lost in Translation." Archives of Pathology & Laboratory Medicine 135, no. 3 (March 1, 2011): 290. http://dx.doi.org/10.5858/2010-0555-le.1.

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Zhang, Ting, Anqi Wu, Yaping Yue, and Yu Zhao. "uORFs: Important Cis-Regulatory Elements in Plants." International Journal of Molecular Sciences 21, no. 17 (August 28, 2020): 6238. http://dx.doi.org/10.3390/ijms21176238.

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Gene expression is regulated at many levels, including mRNA transcription, translation, and post-translational modification. Compared with transcriptional regulation, mRNA translational control is a more critical step in gene expression and allows for more rapid changes of encoded protein concentrations in cells. Translation is highly regulated by complex interactions between cis-acting elements and trans-acting factors. Initiation is not only the first phase of translation, but also the core of translational regulation, because it limits the rate of protein synthesis. As potent cis-regulatory elements in eukaryotic mRNAs, upstream open reading frames (uORFs) generally inhibit the translation initiation of downstream major ORFs (mORFs) through ribosome stalling. During the past few years, with the development of RNA-seq and ribosome profiling, functional uORFs have been identified and characterized in many organisms. Here, we review uORF identification, uORF classification, and uORF-mediated translation initiation. More importantly, we summarize the translational regulation of uORFs in plant metabolic pathways, morphogenesis, disease resistance, and nutrient absorption, which open up an avenue for precisely modulating the plant growth and development, as well as environmental adaption. Additionally, we also discuss prospective applications of uORFs in plant breeding.

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Castro-Roa, Daniel, and Nikolay Zenkin. "Methodology for the analysis of transcription and translation in transcription-coupled-to-translation systems in vitro." Methods 86 (September 2015): 51–59. http://dx.doi.org/10.1016/j.ymeth.2015.05.029.

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Ueguchi, Chiharu, Naoko Misonou, and Takeshi Mizuno. "Negative Control of rpoS Expression by Phosphoenolpyruvate:Carbohydrate Phosphotransferase System inEscherichia coli." Journal of Bacteriology 183, no. 2 (January 15, 2001): 520–27. http://dx.doi.org/10.1128/jb.183.2.520-527.2001.

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ABSTRACT The ςS (or ς38) subunit of RNA polymerase, encoded by the rpoS gene, is a crucial regulator in the transcriptional control of a set of genes under stressful conditions, such as nutrient starvation. The expression ofrpoS is regulated in a complex manner at the levels of transcription, translation, and stability of the product. Although a number of factors involved in the regulation of rpoSexpression have been identified, the underlying molecular mechanisms are not fully understood. In this study, we identified the Crr (or EIIAGlc) protein as a novel factor that plays an important role not only in the transcriptional control but also in the translational control of rpoS expression. Crr is an important component in glucose uptake through the well-characterized phosphoenolpyruvate:carbohydrate phosphotransferase system. The results of a series of genetic analyses revealed that Crr negatively controlsrpoS translation and transcription. The observed transcriptional control by Crr appears to be mediated by cyclic AMP. However, it was found that Crr negatively controls rpoStranslation rather directly. These results suggest a possible linkage between the control of rpoS expression and carbon metabolism.

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Ouellette, A. J., R. Moonka, A. D. Zelenetz, and R. A. Malt. "Regulation of ribosome synthesis during compensatory renal hypertrophy in mice." American Journal of Physiology-Cell Physiology 253, no. 4 (October 1, 1987): C506—C513. http://dx.doi.org/10.1152/ajpcell.1987.253.4.c506.

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Ribosomal synthesis was studied at the transcriptional and translational levels to investigate the mechanisms of ribosome accretion during compensatory renal hypertrophy. As measured by in vitro transcriptional runoff comparisons 6-48 h after surgery, nuclei from the kidney remaining after contralateral nephrectomy show an increase of up to 150% in the rate of synthesis of ribosomal precursor RNA. The rate of rDNA transcription is 40-50% greater than control values as early as 6 h after nephrectomy; by 48 h, the rate returns to normal. In contrast to the stimulated transcription of rDNA and accretion of rRNA, the steady-state levels and the cytoplasmic distribution of ribosomal protein mRNAs S16 and L10 remain unchanged during induced renal growth. Thus coordinate production of adequate protein for increased assembly of ribosomes during induced renal growth appears to be accomplished by increasingly efficient translation of existing ribosomal protein mRNAs or by post-translational stabilization of ribosomal proteins. The rate of rDNA transcription may be regulated by accelerating the transcription of already functioning genes or, more likely, by recruiting transcription units that are transcriptionally inactive in the normal kidney.

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Baird, Thomas D., Lakshmi Reddy Palam, Michael E. Fusakio, Jeffrey A. Willy, Christopher M. Davis, Jeanette N. McClintick, Tracy G. Anthony, and Ronald C. Wek. "Selective mRNA translation during eIF2 phosphorylation induces expression of IBTKα." Molecular Biology of the Cell 25, no. 10 (May 15, 2014): 1686–97. http://dx.doi.org/10.1091/mbc.e14-02-0704.

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Disruption of protein folding in the endoplasmic reticulum (ER) triggers the unfolded protein response (UPR), a transcriptional and translational control network designed to restore protein homeostasis. Central to the UPR is PKR-like ER kinase (PERK/EIF2AK3) phosphorylation of the α subunit of eIF2 (eIF2α∼P), which represses global translation coincident with preferential translation of mRNAs, such as activating transcription factor 4 (ATF4) and C/EBP-homologous protein (CHOP), that serve to implement UPR transcriptional regulation. In this study, we used sucrose gradient ultracentrifugation and a genome-wide microarray approach to measure changes in mRNA translation during ER stress. Our analysis suggests that translational efficiencies vary over a broad range during ER stress, with the majority of transcripts being either repressed or resistant to eIF2α∼P, whereas a notable cohort of key regulators are subject to preferential translation. From the latter group, we identified the α isoform of inhibitor of Bruton's tyrosine kinase (IBTKα) as being subject to both translational and transcriptional induction during eIF2α∼P in both cell lines and a mouse model of ER stress. Translational regulation of IBTKα mRNA involves stress-induced relief of two inhibitory upstream open reading frames in the 5′-leader of the transcript. Depletion of IBTKα by short hairpin RNA reduced viability of cultured cells coincident with increased caspase 3/7 cleavage, suggesting that IBTKα is a key regulator in determining cell fate during the UPR.

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Schemidt, Randy A., Jun Qu, James R. Williams, and William S. A. Brusilow. "Effects of Carbon Source on Expression of Fo Genes and on the Stoichiometry of the c Subunit in the F1Fo ATPase of Escherichia coli." Journal of Bacteriology 180, no. 12 (June 15, 1998): 3205–8. http://dx.doi.org/10.1128/jb.180.12.3205-3208.1998.

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ABSTRACT Expression of the genes for the membrane-bound Fosector of the Escherichia coli F1Foproton-translocating ATPase can respond to changes in metabolic conditions, and these changes are reflected in alterations in the subunit stoichiometry of the oligomeric Fo proton channel. Transcriptional and translational lacZ fusions to the promoter and to two Fo genes show that, during growth on the nonfermentable carbon source succinate, transcription of the operon and translation of uncB, encoding the a subunit of Fo, are higher than during growth on glucose. In contrast, translation of the uncE gene, encoding the c subunit of Fo, is higher during growth on glucose than during growth on succinate. Translation rates of both uncB anduncE change as culture density increases, but transcription rates do not. Quantitation of the c stoichiometry shows that more c subunits are assembled into the F1Fo ATPase in cells grown on glucose than in cells grown on succinate. E. coli therefore appears to have a mechanism for regulating the composition and, presumably, the function of the ATPase in response to metabolic circumstances.

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Zhou, Bing, Maja Semanjski, Natalie Orlovetskie, Saurabh Bhattacharya, Sima Alon, Liron Argaman, Nayef Jarrous, et al. "Arginine dephosphorylation propels spore germination in bacteria." Proceedings of the National Academy of Sciences 116, no. 28 (June 20, 2019): 14228–37. http://dx.doi.org/10.1073/pnas.1817742116.

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Bacterial spores can remain dormant for years but possess the remarkable ability to germinate, within minutes, once nutrients become available. However, it still remains elusive how such instant awakening of cellular machineries is achieved. UtilizingBacillus subtilisas a model, we show that YwlE arginine (Arg) phosphatase is crucial for spore germination. Accordingly, the absence of the Arg kinase McsB accelerated the process. Arg phosphoproteome of dormant spores uncovered a unique set of Arg-phosphorylated proteins involved in key biological functions, including translation and transcription. Consequently, we demonstrate that during germination, YwlE dephosphorylates an Arg site on the ribosome-associated chaperone Tig, enabling its association with the ribosome to reestablish translation. Moreover, we show that Arg dephosphorylation of the housekeeping σ factor A (SigA), mediated by YwlE, facilitates germination by activating the transcriptional machinery. Subsequently, we reveal that transcription is reinitiated at the onset of germination and its recommencement precedes that of translation. Thus, Arg dephosphorylation elicits the most critical stages of spore molecular resumption, placing this unusual post-translational modification as a major regulator of a developmental process in bacteria.

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Aguilera, G., S. Volpi, and C. Rabadan-Diehl. "Transcriptional and post-transcriptional mechanisms regulating the rat pituitary vasopressin V1b receptor gene." Journal of Molecular Endocrinology 30, no. 2 (April 1, 2003): 99–108. http://dx.doi.org/10.1677/jme.0.0300099.

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The number of V1b vasopressin receptors (V1bR) in the anterior pituitary plays an important role during adaptation of the hypothalamic-pituitary-adrenal axis to stress in rats. Regulation of V1bR expression involves transcriptional and translational mechanisms. One of the elements mediating transcriptional activation of the rat V1bR gene is a long stretch of GAGA repeats (GAGA box) in the promoter located near the transcription start point capable of binding a protein complex of 127 kDa present in pituitary nuclear extracts. There is a lack of correlation between changes in V1bR mRNA and the number of VP binding sites, suggesting that V1bR expression depends on the efficiency of V1b R mRNA translation into protein. Two mechanisms by which the 5' untranslated region (5'-UTR) of the rat V1bR mRNA can mediate either inhibition or activation of V1bR mRNA translation have been identified. First, upstream open reading frames (ORF) present in the 5'-UTR repress translation of the major ORF encoding the V1b receptor, and secondly, an internal ribosome entry site (IRES) activates V1bR translation. Stimulation of IRES activity through protein kinase C-mediated pathways results in V1bR mRNA translation increasing V1bR protein levels. The existence of multiple loci of regulation for the V1bR at transcriptional and translational levels provides a mechanism to facilitate plasticity of regulation of the number of pituitary vasopressin receptors according to physiological demand.

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Clayton, Christine. "Regulation of gene expression in trypanosomatids: living with polycistronic transcription." Open Biology 9, no. 6 (June 2019): 190072. http://dx.doi.org/10.1098/rsob.190072.

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In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans -splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.

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Schrader, Jared M., Gene-Wei Li, W. Seth Childers, Adam M. Perez, Jonathan S. Weissman, Lucy Shapiro, and Harley H. McAdams. "Dynamic translation regulation inCaulobactercell cycle control." Proceedings of the National Academy of Sciences 113, no. 44 (October 17, 2016): E6859—E6867. http://dx.doi.org/10.1073/pnas.1614795113.

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Progression of theCaulobactercell cycle requires temporal and spatial control of gene expression, culminating in an asymmetric cell division yielding distinct daughter cells. To explore the contribution of translational control, RNA-seq and ribosome profiling were used to assay global transcription and translation levels of individual genes at six times over the cell cycle. Translational efficiency (TE) was used as a metric for the relative rate of protein production from each mRNA. TE profiles with similar cell cycle patterns were found across multiple clusters of genes, including those in operons or in subsets of operons. Collections of genes associated with central cell cycle functional modules (e.g., biosynthesis of stalk, flagellum, or chemotaxis machinery) have consistent but different TE temporal patterns, independent of their operon organization. Differential translation of operon-encoded genes facilitates precise cell cycle-timing for the dynamic assembly of multiprotein complexes, such as the flagellum and the stalk and the correct positioning of regulatory proteins to specific cell poles. The cell cycle-regulatory pathways that produce specific temporal TE patterns are separate from—but highly coordinated with—the transcriptional cell cycle circuitry, suggesting that the scheduling of translational regulation is organized by the same cyclical regulatory circuit that directs the transcriptional control of theCaulobactercell cycle.

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Hirsch, Matthew, and Thomas Elliott. "Stationary-Phase Regulation of RpoS Translation in Escherichia coli." Journal of Bacteriology 187, no. 21 (November 1, 2005): 7204–13. http://dx.doi.org/10.1128/jb.187.21.7204-7213.2005.

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ABSTRACT In enteric bacteria, adaptation to a number of different stresses is mediated by the RpoS protein, one of several sigma factors that collectively allow a tailored transcriptional response to environmental cues. Stress stimuli including low temperature, osmotic shock, nutrient limitation, and growth to stationary phase (SP) all result in a substantial increase in RpoS abundance and activity. The mechanism of regulation depends on the specific signal but may occur at the level of transcription, translation, protein activity, or targeted proteolysis. In both Escherichia coli and Salmonella enterica, SP induction of RpoS in rich medium is >30 fold and includes effects on both transcription and translation. Recently, we found that SP control of rpoS transcription in S. enterica involves repression of the major rpoS promoter during exponential phase by the global transcription factor Fis. Working primarily with E. coli, we now show that 24 nucleotides of the rpoS ribosome-binding site (RBS) are necessary and sufficient for a large part of the increase in rpoS translation as cells grow to SP. Genetic evidence points to an essential role for the leader nucleotides just upstream of the Shine-Dalgarno sequence but is conflicted on the question of whether sequence or structure is important. SP regulation of rpoS is conserved between E. coli and S. enterica. When combined with an fis mutation to block transcriptional effects, replacement of the rpoS RBS sequence by the lacZ RBS eliminates nearly all SP induction of RpoS.

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Nou, Xiangwu, and Robert J. Kadner. "Coupled Changes in Translation and Transcription during Cobalamin-Dependent Regulation of btuB Expression inEscherichia coli." Journal of Bacteriology 180, no. 24 (December 15, 1998): 6719–28. http://dx.doi.org/10.1128/jb.180.24.6719-6728.1998.

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ABSTRACT The level of the vitamin B12 transport protein BtuB in the outer membrane of Escherichia coli is strongly reduced by growth in the presence of cobalamins. Previous analyses of regulatory mutants and of btuB-lacZ fusions indicated that the primary site of btuB gene regulation was at the translational level, and this required sequences throughout the 240-nucleotide (nt) leader region. Cobalamin-dependent regulation of transcriptional fusions was of a lesser magnitude but required, in addition to the leader, sequences within the first 100 nt of the coding sequence, termed the translated regulatory region (TRR). To analyze the process of transcription-level regulation of btuB inE. coli, the levels and metabolism of btuB RNA were analyzed by S1 nuclease protection assays, and mutations that alter the coupling of translational and transcriptional control were analyzed. Expression of transcriptional fusions was found to correlate with changes in the level of intact btuB RNA and was related to changes in the metabolic stability of the normally long-lived RNA. Mutational analysis showed that the btuBstart codon and a hairpin structure that can sequester the Shine-Dalgarno sequence are necessary for cobalamin-dependent regulation and that translation of the TRR is necessary for extended RNA stability and for expression of the transcriptional fusion. The absence of regulation at the stage of transcription initiation was confirmed by the findings that several truncated btuB RNA fragments were expressed in a constitutive manner and that the normal regulatory response occurred even when thebtuB promoter and upstream sequences were replaced by the heterologous bla and lac promoters. Transcription driven by phage T7 RNA polymerase was not regulated by cobalamins, although some regulation at the translational level was retained. Cobalamin-dependent changes in RNA structure were suggested from the RNase III-dependent production of a transcript fragment that is made only in the presence of cobalamin and is independent of the regulatory outcome. These results indicate that the primary control ofbtuB expression by cobalamin occurs at the level of translation initiation, which directly affects the level and stability of btuB RNA in a process that requires the presence of the intact translated regulatory region.

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Yost, Christian C., Melvin M. Denis, Stephan Lindemann, Frederick J. Rubner, Gopal K. Marathe, Michael Buerke, Thomas M. McIntyre, Andrew S. Weyrich, and Guy A. Zimmerman. "Activated Polymorphonuclear Leukocytes Rapidly Synthesize Retinoic Acid Receptor-α." Journal of Experimental Medicine 200, no. 5 (August 30, 2004): 671–80. http://dx.doi.org/10.1084/jem.20040224.

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In addition to releasing preformed granular proteins, polymorphonuclear leukocytes (PMNs) synthesize chemokines and other factors under transcriptional control. Here we demonstrate that PMNs express an inducible transcriptional modulator by signal-dependent activation of specialized mechanisms that regulate messenger RNA (mRNA) translation. HL-60 myelocytic cells differentiated to surrogate PMNs respond to activation by platelet activating factor by initiating translation and with appearance of specific mRNA transcripts in polyribosomes. cDNA array analysis of the polyribosome fraction demonstrated that retinoic acid receptor (RAR)-α, a transcription factor that controls the expression of multiple genes, is one of the polyribosome-associated transcripts. Quiescent surrogate HL60 PMNs and primary human PMNs contain constitutive message for RAR-α but little or no protein. RAR-α protein is rapidly synthesized in response to platelet activating factor under the control of a specialized translational regulator, mammalian target of rapamycin, and is blocked by the therapeutic macrolide rapamycin, events consistent with features of the 5′ untranslated region of the transcript. Newly synthesized RAR-α modulates production of interleukin-8. Rapid expression of a transcription factor under translational control is a previously unrecognized mechanism in human PMNs that indicates unexpected diversity in gene regulation in this critical innate immune effector cell.

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Journal articles on the topic 'Transcription and translation'

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