Gfh factors and NusA cooperate to stimulate transcriptional pausing and termination

Agapov, Aleksei; Олина, А. А.; Esyunina, Daria; Kulbachinskiy, Andrey

doi:10.1002/1873-3468.12609

Cited by 8 publications

(4 citation statements)

References 41 publications

(105 reference statements)

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“…Interestingly also circadian clock related proteins are represented in the Reactome pathways, reinforcing the link between muscle differentiation or regeneration and synchronization as already published. STRING analysis (http://string-db.org) [24][25][26] of network nodes involving the scored 37 human TFs identified experimentally determined interaction among the TFs supporting the bioinformatics analysis performed on DMI52 pausing site (Fig. S7).…”

Section: Bioinformatics Analysis Of the Dmi52 Regionsupporting

confidence: 57%

Transcriptional and epigenetic analyses of the DMD locus reveal novel cis ‑acting DNA elements that govern muscle dystrophin expression

Gherardi

Bovolenta

Passarelli

et al. 2017

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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The dystrophin gene (DMD) is the largest gene in the human genome, mapping on the Xp21 chromosome locus. It spans 2.2Mb and accounts for approximately 0,1% of the entire human genome. Mutations in this gene cause Duchenne and Becker Muscular Dystrophy, X-linked Dilated Cardiomyopathy, and other milder muscle phenotypes. Beside the remarkable number of reports describing dystrophin gene expression and the pathogenic consequences of the gene mutations in dystrophinopathies, the full scenario of the DMD transcription dynamics remains however, poorly understood. Considering that the full transcription of the DMD gene requires about 16h, we have investigated the activity of RNA Polymerase II along the entire DMD locus within the context of specific chromatin modifications using a variety of chromatin-based techniques. Our results unveil a surprisingly powerful processivity of the RNA polymerase II along the entire 2.2Mb of the DMD locus with just one site of pausing around intron 52. We also discovered epigenetic marks highlighting the existence of four novel cis‑DNA elements, two of which, located within intron 34 and exon 45, appear to govern the architecture of the DMD chromatin with implications on the expression levels of the muscle dystrophin mRNA. Overall, our findings provide a global view on how the entire DMD locus is dynamically transcribed by the RNA pol II and shed light on the mechanisms involved in dystrophin gene expression control, which can positively impact on the optimization of the novel ongoing therapeutic strategies for dystrophinopathies.

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Section: Bioinformatics Analysis Of the Dmi52 Regionsupporting

confidence: 57%

Transcriptional and epigenetic analyses of the DMD locus reveal novel cis ‑acting DNA elements that govern muscle dystrophin expression

Gherardi

Bovolenta

Passarelli

et al. 2017

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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“…While prototypical bacterial RNA polymerases are thought to be magnesium-dependent 51 , RNA polymerases purified from the Firmicutes (Clostridium acetobutylicum, Bacillus subtilis, and Lactobacillus curvatus) are manganese-dependent 40,52,53 . A regulatory role for manganese has been demonstrated for some previously characterized RNA polymerases, such as transcription stalling, while others seem to require manganese for catalytic activity 40,[51][52][53][54][55][56] . Although the highest level of activity from the B. burgdorferi RNA polymerase was obtained from a combination of magnesium and manganese, the role of manganese in catalysis remains unexplored; note that the conserved catalytic site amino acid residues do not differ between magnesium-and manganese-utilizing bacteria.…”

Section: Discussionmentioning

confidence: 99%

Establishment of an in vitro RNA polymerase transcription system: a new tool to study transcriptional activation in Borrelia burgdorferi

Boyle

Hall

Armstrong

et al. 2020

Sci Rep

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The Lyme disease spirochete Borrelia burgdorferi exhibits dramatic changes in gene expression as it transits between its tick vector and vertebrate host. A major hurdle to understanding the mechanisms underlying gene regulation in B. burgdorferi has been the lack of a functional assay to test how gene regulatory proteins and sigma factors interact with RnA polymerase to direct transcription. to gain mechanistic insight into transcriptional control in B. burgdorferi, and address sigma factor function and specificity, we developed an in vitro transcription assay using the B. burgdorferi RnA polymerase holoenzyme. We established reaction conditions for maximal RnA polymerase activity by optimizing pH, temperature, and the requirement for divalent metals. Using this assay system, we analyzed the promoter specificity of the housekeeping sigma factor RpoD to promoters encoding previously identified RpoD consensus sequences in B. burgdorferi. Collectively, this study established an in vitro transcription assay that revealed RpoD-dependent promoter selectivity by RNA polymerase and the requirement of specific metal cofactors for maximal RNA polymerase activity. The establishment of this functional assay will facilitate molecular and biochemical studies on how gene regulatory proteins and sigma factors exert control of gene expression in B. burgdorferi required for the completion of its enzootic cycle. Borrelia burgdorferi is a highly fastidious host-associated bacterium in the phylum Spirochaetes 1,2. B. burgdorferi is adapted to a vector-host life cycle and possesses a condensed 1.3 Mb genome with limited metabolic capability 3,4. The genome lacks genes encoding components of the citric acid cycle, the electron transport chain, amino acid biosynthesis, and fatty acid biosynthesis pathways, wholly relying on the transport of sugars, fatty acids and amino acids from the environment for survival 5,6. B. burgdorferi growth occurs extracellularly in vertebrate tissues and in ticks following a blood meal, which poses additional nutritional constraints 7. In particular, the host competition for iron is hypothesized to have resulted in abstinence from iron utilization by B. burgdorferi 8-10. Instead, manganese is thought to largely replace iron as a metal cofactor for metabolic enzymes 9,11. B. burgdorferi regulates gene expression to adapt to environmental constraints faced in its enzootic cycle. B. burgdorferi responds to environmental changes in pH, temperature, nutrient availability, and manganese levels with dramatic shifts in transcription and growth 12-18. The transcriptional changes in B. burgdorferi during transmission from the arthropod vector Ixodes scapularis 19,20 are thought to be influenced by the mechanisms underlying environmental sensing and transcriptional responses. Mechanistic studies of how transcription factors regulate gene expression in B. burgdorferi have been hindered by the scarcity of biochemical tools. To understand the transcriptional mechanisms that support B. burgdorferi survival, we set out to ...

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“…The spirochete regulates the cellular concentrations of manganese through the BmtA transporter (Ouyang et al, 2009a;Wagh et al, 2015), and alterations in extracellular levels of manganese affect the expression of a variety of virulence genes . Changes in B. burgdorferi gene expression in response to lower concentrations of manganese may be the consequence of reducing the bioavailability of manganese required for RNA polymerase activity, resulting in transcriptional stalling as described in other bacteria (Rutberg and Armentrout, 1972;Stetter and Zillig, 1974;Borbely and Schneider, 1988;Pich and Bahl, 1991;Sosunov et al, 2003;Poranen et al, 2008;Agapov et al, 2017).…”

Section: Rna Polymerasementioning

confidence: 97%

Gene Regulation and Transcriptomics

Samuels¹,

Lybecker²,

Yang³

et al. 2022

Current Issues in Molecular Biology

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Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma (σ) factor cascade, the Hk1/Rrp1 twocomponent system and its product c-di-GMP, and the stringent response mediated by RelBbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or finetuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by highthroughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each. caister.com/cimb 223 Curr. Issues Mol. Biol. Vol. 42 Curr. Issues Mol. Biol. 42: 223-266. caister.com/cimb Gene Regulation and Transcriptomics Samuels et al.Figure 2. A model of the RpoN-RpoS σ factor cascade. During tick feeding and mammalian infection, environmental and host signals activate the RpoN-RpoS σ factor cascade. Activation of RpoN requires phosphorylation of Rrp2 and accumulation of BosR. Rrp2 is the sole prokaryotic enhancer-binding protein present in B. burgdorferi that is required for RpoN (σ 54 ) activation. Phosphorylation of Rrp2 not only is required for RpoN-RpoS activation, but also is indispensable for cell survival, presumably replication. Levels of BosR respond to environmental signals and accumulation of BosR activates rpoS at its RpoN-dependent promoter via an unknown mechanism. BadR represses rpoS transcription by directly binding near the RpoN-dependent promoter region. In addition to the major rpoS mRNA species transcribed from the RpoN-dependent promoter, a longer rpoS transcript is produced at low cell density from an RpoN-independent promoter located within the upstream flgJ gene. The sRNA DsrABb regulates the efficiency of long rpoS mRNA species translation in response to temperature. DDB18 can regulate RpoS (σ S ) levels at the post-transcriptional level. Accumulation of rpoS transcript leads to the production of OspC, DbpA, DbpB, BBK32, and other mammalian infection-associated proteins.

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Gfh factors and NusA cooperate to stimulate transcriptional pausing and termination

Cited by 8 publications

References 41 publications

Transcriptional and epigenetic analyses of the DMD locus reveal novel cis ‑acting DNA elements that govern muscle dystrophin expression

Transcriptional and epigenetic analyses of the DMD locus reveal novel cis ‑acting DNA elements that govern muscle dystrophin expression

Establishment of an in vitro RNA polymerase transcription system: a new tool to study transcriptional activation in Borrelia burgdorferi

Gene Regulation and Transcriptomics

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