Relevant bibliographies by topics / Prokaryotic Transcription

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Academic literature on the topic 'Prokaryotic Transcription'

Author: Grafiati
Published: 6 September 2023
Last updated: 31 July 2025

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Journal articles on the topic "Prokaryotic Transcription"

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Chávez, Joselyn, Damien P. Devos, and Enrique Merino. "Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea." Journal of Bacteriology 203, no. 2 (2020): e00413-20. http://dx.doi.org/10.1128/jb.00413-20.

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ABSTRACTIn prokaryotes, the key players in transcription initiation are sigma factors and transcription factors that bind to DNA to modulate the process, while premature transcription termination at the 5′ end of the genes is regulated by attenuation and, in particular, by attenuation associated with riboswitches. In this study, we describe the distribution of these regulators across phylogenetic groups of bacteria and archaea and find that their abundance not only depends on the genome size, as previously described, but also varies according to the phylogeny of the organism. Furthermore, we o
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Dixit, Vidula, Elisabetta Bini, Melissa Drozda, and Paul Blum. "Mercury Inactivates Transcription and the Generalized Transcription Factor TFB in the Archaeon Sulfolobus solfataricus." Antimicrobial Agents and Chemotherapy 48, no. 6 (2004): 1993–99. http://dx.doi.org/10.1128/aac.48.6.1993-1999.2004.

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ABSTRACT Mercury has a long history as an antimicrobial agent effective against eukaryotic and prokaryotic organisms. Despite its prolonged use, the basis for mercury toxicity in prokaryotes is not well understood. Archaea, like bacteria, are prokaryotes but they use a simplified version of the eukaryotic transcription apparatus. This study examined the mechanism of mercury toxicity to the archaeal prokaryote Sulfolobus solfataricus. In vivo challenge with mercuric chloride instantaneously blocked cell division, eliciting a cytostatic response at submicromolar concentrations and a cytocidal re
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Goodrich, James A., and William R. McClure. "Competing promoters in prokaryotic transcription." Trends in Biochemical Sciences 16 (January 1991): 394–97. http://dx.doi.org/10.1016/0968-0004(91)90162-o.

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Pruss, Gail J., and Karl Drlica. "DNA supercoiling and prokaryotic transcription." Cell 56, no. 4 (1989): 521–23. http://dx.doi.org/10.1016/0092-8674(89)90574-6.

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Decker, Katherine T., Ye Gao, Kevin Rychel, et al. "proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms." Nucleic Acids Research 50, no. D1 (2021): D1077—D1084. http://dx.doi.org/10.1093/nar/gkab1043.

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Abstract The transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motiva
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Zheng, Ming, and Gisela Storz. "Redox sensing by prokaryotic transcription factors." Biochemical Pharmacology 59, no. 1 (2000): 1–6. http://dx.doi.org/10.1016/s0006-2952(99)00289-0.

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Hwang, Seungha, Jimin Lee, and Jin Young Kang. "Prokaryotic transcription regulation by the nascent RNA elements." Korean Society for Structural Biology 8, no. 2 (2020): 33–40. http://dx.doi.org/10.34184/kssb.2020.8.2.33.

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Jacques, J. P., and D. Kolakofsky. "Pseudo-templated transcription in prokaryotic and eukaryotic organisms." Genes & Development 5, no. 5 (1991): 707–13. http://dx.doi.org/10.1101/gad.5.5.707.

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Chetal, Kashish, and Sarath Chandra Janga. "OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/318217.

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Background. In prokaryotic organisms, a substantial fraction of adjacent genes are organized into operons—codirectionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Although several available operon databases provide information with varying levels of reliability, very few resources provide experimentally supported results. Therefore, we believe that the biological community could benefit from having a new operon prediction database with operons predicted using next-generation RNA-seq datasets.Description. We present operomeDB, a database whic
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Jones, Daniel L., Robert C. Brewster, and Rob Phillips. "Promoter architecture dictates cell-to-cell variability in gene expression." Science 346, no. 6216 (2014): 1533–36. http://dx.doi.org/10.1126/science.1255301.

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Variability in gene expression among genetically identical cells has emerged as a central preoccupation in the study of gene regulation; however, a divide exists between the predictions of molecular models of prokaryotic transcriptional regulation and genome-wide experimental studies suggesting that this variability is indifferent to the underlying regulatory architecture. We constructed a set of promoters in Escherichia coli in which promoter strength, transcription factor binding strength, and transcription factor copy numbers are systematically varied, and used messenger RNA (mRNA) fluoresc
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Dissertations / Theses on the topic "Prokaryotic Transcription"

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Martins, Leonardo Pedro Donas-Boto de Vilhena. "Stochastic model of transcription initiation of closely spaced promoters in escherichia coli." Master's thesis, Faculdade de Ciências e Tecnologia, 2011. http://hdl.handle.net/10362/7009.

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Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica<br>The regulatory mechanisms of transcription allow organisms to quickly adapt to changes in their environment and often act during transcription initiation. Here, a stochastic model of transcription initiation at the nucleotide level is proposed to study the dynamics of RNA production in closely spaced promoters and their regulatory mechanisms. We study how different arrangements (convergent e divergent), distance between transcription start sites (TSS), and various kinetic parameters affect the dynamics of RNA production.
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Bandekar, Aditya C. "Cell Cycle Associated Gene Expression Predicts Function in Mycobacteria." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1068.

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While the major events in prokaryotic cell cycle progression are likely to be coordinated with transcriptional and metabolic changes, these processes remain poorly characterized. Unlike many rapidly-growing bacteria, DNA replication and cell division are temporally-resolved in mycobacteria, making these slow-growing organisms a potentially useful system to investigate the prokaryotic cell cycle. To determine if cell-cycle dependent gene regulation occurs in mycobacteria, we characterized the temporal changes in the transcriptome of synchronously replicating populations of Mycobacterium tubercu
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Dian, Cyril. "Adaptive Responses by Transcriptional Regulators to small molecules in Prokaryotes : Structural studies of two bacterial one-component signal transduction systems DntR and HpNikR." Doctoral thesis, Stockholm : Department of Biochemistry and Biophysics, Stockholm University, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7052.

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Elison, Kalman Grim. "Purification, functional characterization and crystallization of the PerR peroxide sensor from Saccharopolyspora erythraea." Thesis, Uppsala universitet, Strukturbiologi, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-387943.

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This report summarizes the work on the cloning, expression, and purification of PerR, a metal sensing regulator from Saccharopolyspora erythraea and the subsequent characterization using small angle X-ray scattering and other biochemical methods. The report aims to provide an insight into prokaryotic metal homeostasis, provide a better understanding of how PerR works and provide valuable information for the continued work on the crystallization of PerR.
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Ott, Alban. "Approches bioinformatiques pour identifier et caractériser les ARN régulateurs chez les procaryotes." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112029.

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L’objectif de cette thèse était de progresser dans la compréhension de la régulation génique ARN‑dépendante chez les procaryotes. Le développement de nouvelles approches bioinformatiques a permis de découvrir de nouveaux ARN régulateurs non-codant (ARNrnc), de les caractériser notamment évolutivement et d’identifier leurs cibles putatives. Les ARNrnc ont en commun de pouvoir modifier l’abondance de certaines protéines en interagissant avec l’ARN messager (ARNm) qui les code. Cet effet peut être obtenu selon divers modes d’action qui mènent à la distinction de trois classes d’ARNrnc, les petits
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Aditya, Kumar *. "Structural Feature of Prokaryotic Promoters and their Role in Gene Expression." Thesis, 2015. http://etd.iisc.ac.in/handle/2005/3528.

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Transcription initiation is an important step in the process of gene regulation in prokaryotes. Promoters are stretches of DNA sequence that are present in the upstream region of transcription start sites (TSSs), where RNA polymerase and other transcription factors bind to initiate transcription. Recent advancement in sequencing technologies has resulted in huge amount of raw data in the form of whole genome sequences. This sequence data has to be annotated, in order to identify coding, non-coding and regulatory regions. Computational tools are useful for a quick and fairly reliable annotation
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Aditya, Kumar *. "Structural Feature of Prokaryotic Promoters and their Role in Gene Expression." Thesis, 2015. http://etd.iisc.ernet.in/2005/3528.

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Transcription initiation is an important step in the process of gene regulation in prokaryotes. Promoters are stretches of DNA sequence that are present in the upstream region of transcription start sites (TSSs), where RNA polymerase and other transcription factors bind to initiate transcription. Recent advancement in sequencing technologies has resulted in huge amount of raw data in the form of whole genome sequences. This sequence data has to be annotated, in order to identify coding, non-coding and regulatory regions. Computational tools are useful for a quick and fairly reliable annotation
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Chetal, Kashish. "OperomeDB: database of condition specific transcription in prokaryotic genomes and genomic insights of convergent transcription in bacterial genomes." Thesis, 2014. http://hdl.handle.net/1805/6228.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>My thesis comprises of two individual projects: 1) we have developed a database for operon prediction using high-throughput sequencing datasets for bacterial genomes. 2) Genomics and mechanistic insights of convergent transcription in bacterial genomes. In the first project we developed a database for the prediction of operons for bacterial genomes using RNA-seq datasets, we predicted operons for bacterial genomes. RNA-seq datasets with different condition for each bacterial genome were taken into account and predicted operons usin
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Patel, Twinkal. "Studies on the promoter specificity determinants and modulators of the prokaryotic transcription machinery." Thesis, 2021. https://etd.iisc.ac.in/handle/2005/6040.

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Bacteria adapt to a wide range of environmental conditions by synchronizing transcription with changes in the extracellular environment. This is achieved by the synchronized action of two-component systems, Extra Cytoplasmic Function (ECF) σ factors and myriad one-component systems that combine the roles of both sensors as well as transcription factors. While two-component systems correlate histidine kinase activity with changes in the transcription of target genes, in the case of ECF σ factors, this signal transduction is brought about by the release of free σ factors in the bacterial cell up
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Vogel, Sabine Katja [Verfasser]. "Mechanistic studies on transcription activation via DNA looping in a prokaryotic promoter-enhancer system / presented by Sabine Katja Vogel." 2004. http://d-nb.info/972519467/34.

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Books on the topic "Prokaryotic Transcription"

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Transcription Regulation in Prokaryotes. Oxford University Press, USA, 2000.

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Zürich, Eidgenössische Technische Hochschule, ed. Engineering of prokaryotic transcription regulators for mammalian cell biotechnology. 2003.

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Kirchman, David L. Genomes and meta-omics for microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0005.

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The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacte
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Book chapters on the topic "Prokaryotic Transcription"

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Sybers, David, Daniel Charlier, and Eveline Peeters. "In Vitro Transcription Assay for Archaea Belonging to Sulfolobales." In Prokaryotic Gene Regulation. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2413-5_6.

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Seshasayee, Aswin Sai Narain, Karthikeyan Sivaraman, and Nicholas M. Luscombe. "An Overview of Prokaryotic Transcription Factors." In Subcellular Biochemistry. Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-90-481-9069-0_2.

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Ledesma, Leonardo, Rafael Hernandez-Guerrero, and Ernesto Perez-Rueda. "Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes." In Prokaryotic Gene Regulation. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2413-5_7.

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Hilchey, S., J. Xu, and G. B. Koudelka. "Indirect Effects of DNA Sequence on Transcriptional Activation by Prokaryotic DNA Binding Proteins." In Mechanisms of Transcription. Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60691-5_9.

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Bernauw, Amber Joka, Veerke De Kock, and Indra Bervoets. "In Vivo Screening Method for the Identification and Characterization of Prokaryotic, Metabolite-Responsive Transcription Factors." In Prokaryotic Gene Regulation. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2413-5_8.

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Buc, H. "Initiation of Prokaryotic Transcription-Kinetic and Structural Approaches." In Nucleic Acids and Molecular Biology. Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-46596-3_11.

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Kigawa, Takanori. "Cell-Free Protein Preparation Through Prokaryotic Transcription–Translation Methods." In Methods in Molecular Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-331-2_1.

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Jiang, Xue, Kekely Bruno Attiogbe, Yating Guo, and Xiaoyun Wu. "Production of Double-Stranded RNA Using the Prokaryotic Promoter-Mediated Bidirectional Transcription." In Double-Stranded RNA. Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-3702-9_8.

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Oehler, Stefan, and Benno Müller-Hill. "Prokaryotic control of transcription: How and why does it differ from eukaryotic control?" In Inducible Gene Expression, Volume 1. Birkhäuser Boston, 1995. http://dx.doi.org/10.1007/978-1-4684-6840-3_1.

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Laub, Michael T., and R. Frank Rosenzweig. "Transcriptional Profiling in Bacteria Using Microarrays." In Prokaryotic Genomics. Birkhäuser Basel, 2003. http://dx.doi.org/10.1007/978-3-0348-8963-6_11.

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Conference papers on the topic "Prokaryotic Transcription"

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Larsen, Jan, Susanne Juhler, Ketil Bernt Sørensen, and Dorthe Skou Pedersen. "The Application of Molecular Microbiological Methods for Early Warning of MIC in Pipelines." In CORROSION 2013. NACE International, 2013. https://doi.org/10.5006/c2013-02029.

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Abstract Microbiological measurements performed during routine inspection in the Danish Sector of the North Sea showed that two multiphase pipelines were in risk of microbiologically influenced corrosion (MIC) due to high numbers of troublesome methanogens and sulfate-reducing prokaryotes (SRP). Modeling of test results (based on quantitative PCR [qPCR]) when performing a MIC risk assessment showed that the time required for pitting corrosion to start in the two pipelines was 544 days and 860 days assuming exponential growth of methanogens and SRP. Therefore, it was decided to determine whethe
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Price, Andy, Laura Acuña Álvarez, Corinne Whitby, and Jan Larsen. "Detection of SRP Activity by Quantification of mRNA for the Dissimilatory (Bi) Sulfite Reductase Gene (dsrA) by Reverse Transcription Quantitative PCR." In CORROSION 2010. NACE International, 2010. https://doi.org/10.5006/c2010-10253.

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Abstract Molecular biological methods have been used for some years to identify and quantify active microorganisms present in a commercial oil reservoir where biogenic sulfide production is routinely controlled by nitrate injection. In order to gain a more complete understanding of the effects of nitrate injection on the activity of sulfate reducing prokaryotes (SRP, (which encompasses sulfate reducing Bacteria (SRB)) and sulfate reducing Archaea (SRA)), the mRNA for dsrA present in produced water samples was quantified by reverse transcription quantitative PCR (RT-qPCR); mRNA for dsrA should
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Ni, Chung-En, Duy-Phuong Doan, Yen-Jung Chiu, and Yen-Hua Huang. "TSSNet – A Deep Neural Network Model for Predicting Prokaryotic Transcription Start Sites." In 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2022. http://dx.doi.org/10.1109/bibe55377.2022.00054.

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Polstein, Lauren R., and Charles A. Gersbach. "Photoregulated Gene Expression in Human Cells With Light-Inducible Engineered Transcription Factors." In ASME 2012 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/sbc2012-80573.

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Systems for controlling gene expression in mammalian cells have a wide range of applications in medicine, biotechnology and basic science. An ideal gene regulatory system would allow for precise and specific control over the magnitude and kinetics of gene expression in space and time, while also exerting minimal influence on other genes and cellular components. Several gene regulatory systems have been developed in which orthogonal transcription machinery from prokaryotes or insects has been imported into mammalian cells and used to control the expression of a specific gene. Despite the transf
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Reports on the topic "Prokaryotic Transcription"

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Schuster, Gadi, and David Stern. Integrated Studies of Chloroplast Ribonucleases. United States Department of Agriculture, 2011. http://dx.doi.org/10.32747/2011.7697125.bard.

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Gene regulation at the RNA level encompasses multiple mechanisms in prokaryotes and eukaryotes, including splicing, editing, endo- and exonucleolytic cleavage, and various phenomena related to small or interfering RNAs. Ribonucleases are key players in nearly all of these post-transcriptional mechanisms, as the catalytic agents. This proposal continued BARD-funded research into ribonuclease activities in the chloroplast, where RNase mutation or deficiency can cause metabolic defects and is often associated with plant chlorosis, embryo or seedling lethality, and/or failure to tolerate nutrient
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