Списки джерел: "Supercoiling Sensitive Transcription (SST)"

1

Ahmed, Wareed, Shruti Menon, Pullela V. D. N. B. Karthik, and Valakunja Nagaraja. "Autoregulation of topoisomerase I expression by supercoiling sensitive transcription." Nucleic Acids Research 44, no. 4 (October 22, 2015): 1541–52. http://dx.doi.org/10.1093/nar/gkv1088.

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Szafran, Marcin Jan, Martyna Gongerowska, Paweł Gutkowski, Jolanta Zakrzewska-Czerwińska, and Dagmara Jakimowicz. "The Coordinated Positive Regulation of Topoisomerase Genes Maintains Topological Homeostasis in Streptomyces coelicolor." Journal of Bacteriology 198, no. 21 (August 22, 2016): 3016–28. http://dx.doi.org/10.1128/jb.00530-16.

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ABSTRACTMaintaining an optimal level of chromosomal supercoiling is critical for the progression of DNA replication and transcription. Moreover, changes in global supercoiling affect the expression of a large number of genes and play a fundamental role in adapting to stress. Topoisomerase I (TopA) and gyrase are key players in the regulation of bacterial chromosomal topology through their respective abilities to relax and compact DNA. Soil bacteria such asStreptomycesspecies, which grow as branched, multigenomic hyphae, are subject to environmental stresses that are associated with changes in chromosomal topology. The topological fluctuations modulate the transcriptional activity of a large number of genes and inStreptomycesare related to the production of antibiotics. To better understand the regulation of topological homeostasis inStreptomyces coelicolor, we investigated the interplay between the activities of the topoisomerase-encoding genestopAandgyrBA. We show that the expression of both genes is supercoiling sensitive. Remarkably, increased chromosomal supercoiling induces thetopApromoter but only slightly influencesgyrBAtranscription, while DNA relaxation affects thetopApromoter only marginally but strongly activates thegyrBAoperon. Moreover, we showed that exposure to elevated temperatures induces rapid relaxation, which results in changes in the levels of both topoisomerases. We therefore propose a unique mechanism ofS. coelicolorchromosomal topology maintenance based on the supercoiling-dependent stimulation, rather than repression, of the transcription of both topoisomerase genes. These findings provide important insight into the maintenance of topological homeostasis in an industrially important antibiotic producer.IMPORTANCEWe describe the unique regulation of genes encoding two topoisomerases, topoisomerase I (TopA) and gyrase, in a modelStreptomycesspecies. Our studies demonstrate the coordination of topoisomerase gene regulation, which is crucial for maintenance of topological homeostasis.Streptomycesspecies are producers of a plethora of biologically active secondary metabolites, including antibiotics, antitumor agents, and immunosuppressants. The significant regulatory factor controlling the secondary metabolism is the global chromosomal topology. Thus, the investigation of chromosomal topology homeostasis inStreptomycesstrains is crucial for their use in industrial applications as producers of secondary metabolites.

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Dorman, Charles J. "Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription." Biochemical Society Transactions 41, no. 2 (March 21, 2013): 542–47. http://dx.doi.org/10.1042/bst20120222.

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DNA supercoiling and NAPs (nucleoid-associated proteins) contribute to the regulation of transcription of many bacterial genes. The horizontally acquired SPI (Salmonella pathogenicity island) genes respond positively to DNA relaxation, they are activated and repressed by the Fis (factor for inversion stimulation) and H-NS (histone-like nucleoid-structuring) NAPs respectively, and are positively controlled by the OmpR global regulatory protein. The ompR gene is autoregulated and responds positively to DNA relaxation. Binding of the Fis and OmpR proteins to their targets in DNA is differentially sensitive to its topological state, whereas H-NS binds regardless of the topological state of the DNA. These data illustrate the overlapping and complex nature of NAP and DNA topological contributions to transcription control in bacteria.

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Bateman, E., and M. R. Paule. "Events during eucaryotic rRNA transcription initiation and elongation: conversion from the closed to the open promoter complex requires nucleotide substrates." Molecular and Cellular Biology 8, no. 5 (May 1988): 1940–46. http://dx.doi.org/10.1128/mcb.8.5.1940-1946.1988.

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Chemical footprinting and topological analysis were carried out on the Acanthamoeba castellanii rRNA transcription initiation factor (TIF) and RNA polymerase I complexes with DNA during transcription initiation and elongation. The results show that the binding of TIF and polymerase to the promoter does not alter the supercoiling of the DNA template and the template does not become sensitive to modification by diethylpyrocarbonate, which can identify melted DNA regions. Thus, in contrast to bacterial RNA polymerase, the eucaryotic RNA polymerase I-promoter complex is in a closed configuration preceding addition of nucleotides in vitro. Initiation and 3'-O-methyl CTP-limited translocation by RNA polymerase I results in separation of the polymerase-TIF footprints, leaving the TIF footprint unaltered. In contrast, initiation and translocation result in a significant change in the conformation of the polymerase-DNA complex, culminating in an unwound DNA region of at least 10 base pairs.

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5

Bateman, E., and M. R. Paule. "Events during eucaryotic rRNA transcription initiation and elongation: conversion from the closed to the open promoter complex requires nucleotide substrates." Molecular and Cellular Biology 8, no. 5 (May 1988): 1940–46. http://dx.doi.org/10.1128/mcb.8.5.1940.

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Chemical footprinting and topological analysis were carried out on the Acanthamoeba castellanii rRNA transcription initiation factor (TIF) and RNA polymerase I complexes with DNA during transcription initiation and elongation. The results show that the binding of TIF and polymerase to the promoter does not alter the supercoiling of the DNA template and the template does not become sensitive to modification by diethylpyrocarbonate, which can identify melted DNA regions. Thus, in contrast to bacterial RNA polymerase, the eucaryotic RNA polymerase I-promoter complex is in a closed configuration preceding addition of nucleotides in vitro. Initiation and 3'-O-methyl CTP-limited translocation by RNA polymerase I results in separation of the polymerase-TIF footprints, leaving the TIF footprint unaltered. In contrast, initiation and translocation result in a significant change in the conformation of the polymerase-DNA complex, culminating in an unwound DNA region of at least 10 base pairs.

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6

Spirito, F., and L. Bossi. "Long-distance effect of downstream transcription on activity of the supercoiling-sensitive leu-500 promoter in a topA mutant of Salmonella typhimurium." Journal of bacteriology 178, no. 24 (1996): 7129–37. http://dx.doi.org/10.1128/jb.178.24.7129-7137.1996.

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7

Free, Andrew, and Charles J. Dorman. "Escherichia coli tyrT gene transcription is sensitive to DNA supercoiling in its native chromosomal context: effect of DNA topoisomerase IV overexpression on tyrT promoter function." Molecular Microbiology 14, no. 1 (October 1994): 151–61. http://dx.doi.org/10.1111/j.1365-2958.1994.tb01275.x.

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Sutormin, Dmitry, Alina Galivondzhyan, Azamat Gafurov, and Konstantin Severinov. "Single-nucleotide resolution detection of Topo IV cleavage activity in the Escherichia coli genome with Topo-Seq." Frontiers in Microbiology 14 (April 6, 2023). http://dx.doi.org/10.3389/fmicb.2023.1160736.

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Topoisomerase IV (Topo IV) is the main decatenation enzyme in Escherichia coli; it removes catenation links that are formed during DNA replication. Topo IV binding and cleavage sites were previously identified in the E. coli genome with ChIP-Seq and NorfIP. Here, we used a more sensitive, single-nucleotide resolution Topo-Seq procedure to identify Topo IV cleavage sites (TCSs) genome-wide. We detected thousands of TCSs scattered in the bacterial genome. The determined cleavage motif of Topo IV contained previously known cleavage determinants (−4G/+8C, −2A/+6 T, −1 T/+5A) and additional, not observed previously, positions −7C/+11G and −6C/+10G. TCSs were depleted in the Ter macrodomain except for two exceptionally strong non-canonical cleavage sites located in 33 and 38 bp from the XerC-box of the dif-site. Topo IV cleavage activity was increased in Left and Right macrodomains flanking the Ter macrodomain and was especially high in the 50–60 kb region containing the oriC origin of replication. Topo IV enrichment was also increased downstream of highly active transcription units, indicating that the enzyme is involved in relaxation of transcription-induced positive supercoiling.

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Portman, James R., M. Zuhaib Qayyum, Katsuhiko S. Murakami, and Terence R. Strick. "On the stability of stalled RNA polymerase and its removal by RapA." Nucleic Acids Research, July 12, 2022. http://dx.doi.org/10.1093/nar/gkac558.

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Abstract Stalling of the transcription elongation complex formed by DNA, RNA polymerase (RNAP) and RNA presents a serious obstacle to concurrent processes due to the extremely high stability of the DNA-bound polymerase. RapA, known to remove RNAP from DNA in an ATP-dependent fashion, was identified over 50 years ago as an abundant binding partner of RNAP; however, its mechanism of action remains unknown. Here, we use single-molecule magnetic trapping assays to characterize RapA activity and begin to specify its mechanism of action. We first show that stalled RNAP resides on DNA for times on the order of 106 seconds and that increasing positive torque on the DNA reduces this lifetime. Using stalled RNAP as a substrate we show that the RapA protein stimulates dissociation of stalled RNAP from positively supercoiled DNA but not negatively supercoiled DNA. We observe that RapA-dependent RNAP dissociation is torque-sensitive, is inhibited by GreB and depends on RNA length. We propose that stalled RNAP is dislodged from DNA by RapA via backtracking in a supercoiling- and torque-dependent manner, suggesting that RapA’s activity on transcribing RNAP in vivo is responsible for resolving conflicts between converging polymerase molecular motors.

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Testone, Giulio, Anatoly Petrovich Sobolev, Giovanni Mele, Chiara Nicolodi, Maria Gonnella, Giuseppe Arnesi, Tiziano Biancari, and Donato Giannino. "Leaf nutrient content and transcriptomic analyses of endive (Cichorium endivia) stressed by downpour-induced waterlog reveal a gene network regulating kestose and inulin contents." Horticulture Research 8, no. 1 (May 1, 2021). http://dx.doi.org/10.1038/s41438-021-00513-2.

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AbstractEndive (Cichorium endivia L.), a vegetable consumed as fresh or packaged salads, is mostly cultivated outdoors and known to be sensitive to waterlogging in terms of yield and quality. Phenotypic, metabolic and transcriptomic analyses were used to study variations in curly- (‘Domari’, ‘Myrna’) and smooth-leafed (‘Flester’, ‘Confiance’) cultivars grown in short-term waterlog due to rainfall excess before harvest. After recording loss of head weights in all cultivars (6-35%), which was minimal in ‘Flester’, NMR untargeted profiling revealed variations as influenced by genotype, environment and interactions, and included drop of total carbohydrates (6–50%) and polyols (3–37%), gain of organic acids (2–30%) and phenylpropanoids (98–560%), and cultivar-specific fluctuations of amino acids (−37 to +15%). The analysis of differentially expressed genes showed GO term enrichment consistent with waterlog stress and included the carbohydrate metabolic process. The loss of sucrose, kestose and inulin recurred in all cultivars and the sucrose-inulin route was investigated by covering over 50 genes of sucrose branch and key inulin synthesis (fructosyltransferases) and catabolism (fructan exohydrolases) genes. The lowered expression of a sucrose gene subset together with that of SUCROSE:SUCROSE-1-FRUCTOSYLTRANSFERASE (1-SST) may have accounted for sucrose and kestose contents drop in the leaves of waterlogged plants. Two anti-correlated modules harbouring candidate hub-genes, including 1-SST, were identified by weighted gene correlation network analysis, and proposed to control positively and negatively kestose levels. In silico analysis further pointed at transcription factors of GATA, DOF, WRKY types as putative regulators of 1-SST.

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