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Journal articles on the topic 'Prokaryotic Transcription'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

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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2

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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3

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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4

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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5

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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7

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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8

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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9

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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10

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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11

Kozobay-Avraham, Limor, Sergey Hosid, and Alexander Bolshoy. "Curvature Distribution in Prokaryotic Genomes." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 4, no. 3 (2004): 361–75. https://doi.org/10.3233/isb-00139.

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DNA curvature is known to play a biological role in gene regulation, in particular, initiation of transcription. We applied the software CURVATURE based on the wedge model to predict whether promoter regions of certain prokaryotes may be characterized by higher intrinsic DNA curvature located within or upstream to these regions. The main purpose was to verify our earlier hypothesis that the DNA curvature plays a biological role in gene regulation in mesophilic as compared to hyperthermophilic prokaryotes, i.e., DNA curvature presumably has a functional adaptive significance determined by tempe

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12

Mackiewicz, Pawel, Agnieszka Gierlik, Maria Kowalczuk, Miroslaw R. Dudek, and Stanislaw Cebrat. "How Does Replication-Associated Mutational Pressure Influence Amino Acid Composition of Proteins?" Genome Research 9, no. 5 (1999): 409–16. http://dx.doi.org/10.1101/gr.9.5.409.

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We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and other mechanisms that introduce asymmetry into prokaryotic chromosomes. In many prokaryotic genomes, each component of mutational pressure affects coding sequences not only in silent positions but also in positions in which changes cause amino acid substitutions in coded proteins. Asy

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13

Tromer, Eelco C., Jolien J. E. van Hooff, Geert J. P. L. Kops, and Berend Snel. "Mosaic origin of the eukaryotic kinetochore." Proceedings of the National Academy of Sciences 116, no. 26 (2019): 12873–82. http://dx.doi.org/10.1073/pnas.1821945116.

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The emergence of eukaryotes from ancient prokaryotic lineages embodied a remarkable increase in cellular complexity. While prokaryotes operate simple systems to connect DNA to the segregation machinery during cell division, eukaryotes use a highly complex protein assembly known as the kinetochore. Although conceptually similar, prokaryotic segregation systems and the eukaryotic kinetochore are not homologous. Here we investigate the origins of the kinetochore before the last eukaryotic common ancestor (LECA) using phylogenetic trees, sensitive profile-versus-profile homology detection, and str

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14

Minaev, Mihail Yu, and Anzhelika A. Makhova. "THE STUDY OF PROKARYOTIC GENE EXPRESSION." Theory and practice of meat processing 3, no. 2 (2018): 40–52. http://dx.doi.org/10.21323/2414-438x-2018-3-2-40-52.

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One of the methods to evaluate the level of gene expression is a real-time quantitative polymerase chain reaction (qPCR). Interest in the study of molecular mechanisms of gene expression and its evaluation in prokaryotes is due to the lack of research on this issue and a number of methodological problems. The paper presents a study of gene expression mechanism in prokaryotes evidence from Aeromonas salmonicida AS1 gyrase B and collagenase genes. As a result of the research, Random primer and oligo (dT) primer (two 3’-terminal nucleotides of the primer complementary to stop codon nucleotides of

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15

Becskei, Attila. "Tuning up Transcription Factors for Therapy." Molecules 25, no. 8 (2020): 1902. http://dx.doi.org/10.3390/molecules25081902.

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The recent developments in the delivery and design of transcription factors put their therapeutic applications within reach, exemplified by cell replacement, cancer differentiation and T-cell based cancer therapies. The success of such applications depends on the efficacy and precision in the action of transcription factors. The biophysical and genetic characterization of the paradigmatic prokaryotic repressors, LacI and TetR and the designer transcription factors, transcription activator-like effector (TALE) and CRISPR-dCas9 revealed common principles behind their efficacy, which can aid the

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16

Hwang, Seungha, Jimin Lee, and Jin Young Kang. "Erratum: Prokaryotic transcription regulation by the nascent RNA elements." BIODESIGN 9, no. 1 (2021): 23. http://dx.doi.org/10.34184/kssb.2021.9.1.23.

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17

Dove, Simon L., J. Keith Joung, and Ann Hochschild. "Activation of prokaryotic transcription through arbitrary protein–protein contacts." Nature 386, no. 6625 (1997): 627–30. http://dx.doi.org/10.1038/386627a0.

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18

Cenatiempo, Y. "Prokaryotic gene expression in vitro: transcription-translation coupled systems." Biochimie 68, no. 4 (1986): 505–15. http://dx.doi.org/10.1016/s0300-9084(86)80195-x.

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19

Hochschild, Ann, and Simon L. Dove. "Protein–Protein Contacts that Activate and Repress Prokaryotic Transcription." Cell 92, no. 5 (1998): 597–600. http://dx.doi.org/10.1016/s0092-8674(00)81126-5.

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20

Dudek, Christian-Alexander, and Dieter Jahn. "PRODORIC: state-of-the-art database of prokaryotic gene regulation." Nucleic Acids Research 50, no. D1 (2021): D295—D302. http://dx.doi.org/10.1093/nar/gkab1110.

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Abstract PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the

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21

Bernardo, Nerea, Isidro Crespo, Anna Cuppari, Wilfried J. J. Meijer, and D. Roeland Boer. "A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53." Acta Crystallographica Section D Structural Biology 79, no. 3 (2023): 259–67. http://dx.doi.org/10.1107/s2059798323001298.

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Transcriptional regulation usually requires the action of several proteins that either repress or activate a promotor of an open reading frame. These proteins can counteract each other, thus allowing tight regulation of the transcription of the corresponding genes, where tight repression is often linked to DNA looping or cross-linking. Here, the tetramerization domain of the bacterial gene repressor Rco from Bacillus subtilis plasmid pLS20 (RcopLS20) has been identified and its structure is shown to share high similarity to the tetramerization domain of the well known p53 family of human tumor

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22

Macadlo, Lauren A., Iskander M. Ibrahim, and Sujith Puthiyaveetil. "Sigma factor 1 in chloroplast gene transcription and photosynthetic light acclimation." Journal of Experimental Botany 71, no. 3 (2019): 1029–38. http://dx.doi.org/10.1093/jxb/erz464.

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Abstract Sigma factors are dissociable subunits of bacterial RNA polymerase that ensure efficient transcription initiation from gene promoters. Owing to their prokaryotic origin, chloroplasts possess a typical bacterial RNA polymerase together with its sigma factor subunit. The higher plant Arabidopsis thaliana contain as many as six sigma factors for the hundred or so of its chloroplast genes. The role of this relatively large number of transcription initiation factors for the miniature chloroplast genome, however, is not fully understood. Using two Arabidopsis T-DNA insertion mutants, we sho

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23

Binas, Oliver, Tatjana Schamber, and Harald Schwalbe. "The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans." Nucleic Acids Research 48, no. 12 (2020): 6970–79. http://dx.doi.org/10.1093/nar/gkaa427.

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Abstract Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in purine and carbon-1 metabolic cycles. Its aptamer domain includes the pfl motif, which features a pseudoknot, impeding rho-independent terminator formation upon stabilization by ZMP interaction. We herein investigate the conformational landscape of transcriptional interme

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24

Ortet, Philippe, Gilles De Luca, David E. Whitworth, and Mohamed Barakat. "P2TF: a comprehensive resource for analysis of prokaryotic transcription factors." BMC Genomics 13, no. 1 (2012): 628. http://dx.doi.org/10.1186/1471-2164-13-628.

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25

Zuo, Yong-chun, and Qian-zhong Li. "The hidden physical codes for modulating the prokaryotic transcription initiation." Physica A: Statistical Mechanics and its Applications 389, no. 19 (2010): 4217–23. http://dx.doi.org/10.1016/j.physa.2010.05.034.

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26

Roy, Sourav Singha, Monobesh Patra, Tarakdas Basu, Rakhi Dasgupta та Angshuman Bagchi. "Evolutionary analysis of prokaryotic heat-shock transcription regulatory protein σ32". Gene 495, № 1 (2012): 49–55. http://dx.doi.org/10.1016/j.gene.2011.12.043.

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27

Chen, Liang-Jwu, and Emil M. Orozco. "Recognition of prokaryotic transcription terminators by spinach chloroplast RNA polymerase." Nucleic Acids Research 16, no. 17 (1988): 8411–31. http://dx.doi.org/10.1093/nar/16.17.8411.

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28

Budarina, Zhanna I., Dmitri V. Nikitin, Nikolay Zenkin, et al. "A new Bacillus cereus DNA-binding protein, HlyIIR, negatively regulates expression of B. cereus haemolysin II." Microbiology 150, no. 11 (2004): 3691–701. http://dx.doi.org/10.1099/mic.0.27142-0.

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Haemolysin II, HlyII, is one of several cytotoxic proteins produced by Bacillus cereus, an opportunistic human pathogen that causes food poisoning. The hlyII gene confers haemolytic activity to Escherichia coli cells. Here a new B. cereus gene, hlyIIR, which is located immediately downstream of hlyII and regulates hlyII expression, is reported. The deduced amino acid sequence of HlyIIR is similar to prokaryotic DNA-binding transcriptional regulators of the TetR/AcrA family. Measurements of haemolytic activity levels and of hlyII promoter activity levels using gene fusions and primer-extension

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29

Espinal-Enríquez, Jesús, Daniel González-Terán, and Enrique Hernández-Lemus. "The Transcriptional Network Structure of a Myeloid Cell: A Computational Approach." International Journal of Genomics 2017 (2017): 1–12. http://dx.doi.org/10.1155/2017/4858173.

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Understanding the general principles underlying genetic regulation in eukaryotes is an incomplete and challenging endeavor. The lack of experimental information regarding the regulation of the whole set of transcription factors and their targets in different cell types is one of the main reasons to this incompleteness. So far, there is a small set of curated known interactions between transcription factors and their downstream genes. Here, we built a transcription factor network for human monocytic THP-1 myeloid cells based on the experimentally curated FANTOM4 database where nodes are genes a

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30

Tooba Khalid, Aqsa Khalid, and Sikander Ali. "A critical review on the progression of gene expression in prokaryotic and eukaryotic animals." International Journal of Science and Technology Research Archive 3, no. 2 (2022): 060–72. http://dx.doi.org/10.53771/ijstra.2022.3.2.0108.

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This article is totally based on the literature review about gene expression. Gene is the part of the DNA that is responsible for the formation of the genotype and then a phenotype. Gene can only be expressed in case of formation of protein. The process of the gene expression is accomplished in the two steps; Transcription and translation. Transcription is the process of the formation of the mRNA. Transcription proceeds in the three steps. In initiation step the RNA polymerase moves on the unwind DNA strand until the promoter sequence is reached, next is the elongation step in the newly synthe

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31

Wei, Wenping, Yanzhe Shang, Ping Zhang, et al. "Engineering Prokaryotic Transcriptional Activator XylR as a Xylose-Inducible Biosensor for Transcription Activation in Yeast." ACS Synthetic Biology 9, no. 5 (2020): 1022–29. http://dx.doi.org/10.1021/acssynbio.0c00122.

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32

van Hijum, Sacha A. F. T., Marnix H. Medema, and Oscar P. Kuipers. "Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation." Microbiology and Molecular Biology Reviews 73, no. 3 (2009): 481–509. http://dx.doi.org/10.1128/mmbr.00037-08.

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SUMMARY A major part of organismal complexity and versatility of prokaryotes resides in their ability to fine-tune gene expression to adequately respond to internal and external stimuli. Evolution has been very innovative in creating intricate mechanisms by which different regulatory signals operate and interact at promoters to drive gene expression. The regulation of target gene expression by transcription factors (TFs) is governed by control logic brought about by the interaction of regulators with TF binding sites (TFBSs) in cis-regulatory regions. A factor that in large part determines the

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33

Puthiyaveetil, Sujith, Iskander M. Ibrahim, and John F. Allen. "Evolutionary rewiring: a modified prokaryotic gene-regulatory pathway in chloroplasts." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1622 (2013): 20120260. http://dx.doi.org/10.1098/rstb.2012.0260.

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Photosynthetic electron transport regulates chloroplast gene transcription through the action of a bacterial-type sensor kinase known as chloroplast sensor kinase (CSK). CSK represses photosystem I (PS I) gene transcription in PS I light and thus initiates photosystem stoichiometry adjustment. In cyanobacteria and in non-green algae, CSK homologues co-exist with their response regulator partners in canonical bacterial two-component systems. In green algae and plants, however, no response regulator partner of CSK is found. Yeast two-hybrid analysis has revealed interaction of CSK with sigma fac

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34

Park, Kyung-Soon, Young-Soon Jang, Horim Lee, and Jin-Soo Kim. "Phenotypic Alteration and Target Gene Identification Using Combinatorial Libraries of Zinc Finger Proteins in Prokaryotic Cells." Journal of Bacteriology 187, no. 15 (2005): 5496–99. http://dx.doi.org/10.1128/jb.187.15.5496-5499.2005.

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ABSTRACT We have developed a method with prokaryotic organisms that uses randomized libraries of zinc finger-containing artificial transcription factors to induce phenotypic variations and to identify genes involved in the generation of a specific phenotype of interest. Combining chromatin immunoprecipitation experiments and in silico prediction of target DNA binding sequences for the artificial transcription factors, we identified ubiX, whose down-regulation correlates with the thermotolerance phenotype in Escherichia coli. Our results show that randomized libraries of artificial transcriptio

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35

Landick, R. "The regulatory roles and mechanism of transcriptional pausing." Biochemical Society Transactions 34, no. 6 (2006): 1062–66. http://dx.doi.org/10.1042/bst0341062.

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The multisubunit RNAPs (RNA polymerases) found in all cellular life forms are remarkably conserved in fundamental structure, in mechanism and in their susceptibility to sequence-dependent pausing during transcription of DNA in the absence of elongation regulators. Recent studies of both prokaryotic and eukaryotic transcription have yielded an increasing appreciation of the extent to which gene regulation is accomplished during the elongation phase of transcription. Transcriptional pausing is a fundamental enzymatic mechanism that underlies many of these regulatory schemes. In some cases, pausi

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36

Murata, Masaharu, Tomo Yamasaki, Mizuo Maeda, and Yoshiki Katayama. "An Artificial Regulation System for DNA-transcription: Learning from Prokaryotic Organisms." Chemistry Letters 33, no. 1 (2004): 4–5. http://dx.doi.org/10.1246/cl.2004.4.

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37

Kim, D. M., and C. Y. Choi. "A Semicontinuous Prokaryotic Coupled Transcription/Translation System Using a Dialysis Membrane." Biotechnology Progress 12, no. 5 (1996): 645–49. http://dx.doi.org/10.1021/bp960052l.

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38

Huffman, Joy L., and Richard G. Brennan. "Prokaryotic transcription regulators: more than just the helix-turn-helix motif." Current Opinion in Structural Biology 12, no. 1 (2002): 98–106. http://dx.doi.org/10.1016/s0959-440x(02)00295-6.

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Bai, J., J. Wang, F. Xue, et al. "proTF: a comprehensive data and phylogenomics resource for prokaryotic transcription factors." Bioinformatics 26, no. 19 (2010): 2493–95. http://dx.doi.org/10.1093/bioinformatics/btq432.

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40

Allfano, Pietro, Flavia Rivellini, Danila Limauro, Carmelo B. Bruni, and M. Stella Carlomagno. "A consensus motif common to all rho-dependent prokaryotic transcription terminators." Cell 64, no. 3 (1991): 553–63. http://dx.doi.org/10.1016/0092-8674(91)90239-u.

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41

Bushhouse, David Z., Jiayu Fu, and Julius B. Lucks. "A universal prokaryotic transcription anti-termination mechanism utilizing nascent RNA structure." Biophysical Journal 123, no. 3 (2024): 167a—168a. http://dx.doi.org/10.1016/j.bpj.2023.11.1116.

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42

Trinh, Vincent, Marie-France Langelier, Jacques Archambault, and Benoit Coulombe. "Structural Perspective on Mutations Affecting the Function of Multisubunit RNA Polymerases." Microbiology and Molecular Biology Reviews 70, no. 1 (2006): 12–36. http://dx.doi.org/10.1128/mmbr.70.1.12-36.2006.

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SUMMARY High-resolution crystallographic structures of multisubunit RNA polymerases (RNAPs) have increased our understanding of transcriptional mechanisms. Based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit RNA polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and eukaryotic enzymes. The observations support many previous hypotheses on the transcriptional pr

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43

Le Berre, Diana, Sylvie Reverchon, Georgi Muskhelishvili, and William Nasser. "Relationship between the Chromosome Structural Dynamics and Gene Expression—A Chicken and Egg Dilemma?" Microorganisms 10, no. 5 (2022): 846. http://dx.doi.org/10.3390/microorganisms10050846.

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Prokaryotic transcription was extensively studied over the last half-century. A great deal of data has been accumulated regarding the control of gene expression by transcription factors regulating their target genes by binding at specific DNA sites. However, there is a significant gap between the mechanistic description of transcriptional control obtained from in vitro biochemical studies and the complexity of transcriptional regulation in the context of the living cell. Indeed, recent studies provide ample evidence for additional levels of complexity pertaining to the regulation of transcript

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44

Karlin, Samuel, and Jan Mrázek. "Predicted Highly Expressed Genes of Diverse Prokaryotic Genomes." Journal of Bacteriology 182, no. 18 (2000): 5238–50. http://dx.doi.org/10.1128/jb.182.18.5238-5250.2000.

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ABSTRACT Our approach in predicting gene expression levels relates to codon usage differences among gene classes. In prokaryotic genomes, genes that deviate strongly in codon usage from the average gene but are sufficiently similar in codon usage to ribosomal protein genes, to translation and transcription processing factors, and to chaperone-degradation proteins are predicted highly expressed (PHX). By these criteria, PHX genes in most prokaryotic genomes include those encoding ribosomal proteins, translation and transcription processing factors, and chaperone proteins and genes of principal

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Du, Pei, Chunbo Lou, Xuejin Zhao, Qihui Wang, Xiangyu Ji, and Weijia Wei. "CRISPR-Based Genetic Switches and Other Complex Circuits: Research and Application." Life 11, no. 11 (2021): 1255. http://dx.doi.org/10.3390/life11111255.

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CRISPR-based enzymes have offered a unique capability to the design of genetic switches, with advantages in designability, modularity and orthogonality. CRISPR-based genetic switches operate on multiple levels of life, including transcription and translation. In both prokaryotic and eukaryotic cells, deactivated CRISPR endonuclease and endoribonuclease have served in genetic switches for activating or repressing gene expression, at both transcriptional and translational levels. With these genetic switches, more complex circuits have been assembled to achieve sophisticated functions including i

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46

Mirkin, Ekaterina V., and Sergei M. Mirkin. "Replication Fork Stalling at Natural Impediments." Microbiology and Molecular Biology Reviews 71, no. 1 (2007): 13–35. http://dx.doi.org/10.1128/mmbr.00030-06.

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SUMMARY Accurate and complete replication of the genome in every cell division is a prerequisite of genomic stability. Thus, both prokaryotic and eukaryotic replication forks are extremely precise and robust molecular machines that have evolved to be up to the task. However, it has recently become clear that the replication fork is more of a hurdler than a runner: it must overcome various obstacles present on its way. Such obstacles can be called natural impediments to DNA replication, as opposed to external and genetic factors. Natural impediments to DNA replication are particular DNA binding

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47

Kjeldgaard, Jette, Sidsel Henriksen, Marianne Thorup Cohn, Søren Aabo, and Hanne Ingmer. "Method Enabling Gene Expression Studies of Pathogens in a Complex Food Matrix." Applied and Environmental Microbiology 77, no. 23 (2011): 8456–58. http://dx.doi.org/10.1128/aem.05471-11.

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ABSTRACTWe describe a simple method for stabilizing and extracting high-quality prokaryotic RNA from meat. Heat and salt stress ofEscherichia coliandSalmonellaspp. in minced meat reproducibly induceddnaKandotsBexpression, respectively, as observed by quantitative reverse transcription-PCR (>5-fold relative changes). Thus, the method is applicable in studies of bacterial gene expression in a meat matrix.

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Chowdhury, Nilkanta, and Angshuman Bagchi. "Comparative analysis of prokaryotic and eukaryotic transcription factors using machine-learning techniques." Bioinformation 14, no. 06 (2018): 315–26. http://dx.doi.org/10.6026/97320630014315.

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Wang, Jian-Ying. "Mathematical relationships among DNA supercoiling, cation concentration, and temperature for prokaryotic transcription." Mathematical Biosciences 151, no. 2 (1998): 155–63. http://dx.doi.org/10.1016/s0025-5564(98)10012-3.

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Perez-Rueda, Ernesto, Rafael Hernandez-Guerrero, Mario Alberto Martinez-Nuñez, Dagoberto Armenta-Medina, Israel Sanchez, and J. Antonio Ibarra. "Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors." PLOS ONE 13, no. 4 (2018): e0195332. http://dx.doi.org/10.1371/journal.pone.0195332.

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