Visualization of a mammalian transcription initiation complex

1992 ◽  
Vol 70 (5) ◽  
pp. 291-300 ◽  
Author(s):  
E. A. Welsh ◽  
P. Zahradka ◽  
D. E. Larson ◽  
B. H. Sells ◽  
G. Harauz

Various proteins required for the initiation of eukaryotic gene transcription by RNA polymerase II have been identified and characterized, but little is known about their organization into a functional unit. Here, we describe the appearance of the murine ribosomal protein (rp) L32 gene transcription initiation complex as determined by transmission electron microscopy. Using a fractionated nuclear extract enriched for transcription factors necessary for rpL32 gene transcription in vitro and a DNA fragment containing the rpL32 gene promoter, the transcription initiation complex was imaged by standard transmission electron microscopy. Quantitative image analysis demonstrated that the complex is a multilobed structure whose two-dimensional projections are approximately 24 × 34 nm in size. Looping of the DNA seen in these images suggests that the proteins residing at the promoter region associate with proteins several hundred base pairs distant to the RNA start site, with bending of the DNA allowing these interactions to occur.Key words: electron microscopy, ribosomal protein gene, gene transcription, transcription factors.

1999 ◽  
Vol 19 (3) ◽  
pp. 2130-2141 ◽  
Author(s):  
T. C. Kuhlman ◽  
H. Cho ◽  
D. Reinberg ◽  
N. Hernandez

ABSTRACT RNA polymerase II transcribes the mRNA-encoding genes and the majority of the small nuclear RNA (snRNA) genes. The formation of a minimal functional transcription initiation complex on a TATA-box-containing mRNA promoter has been well characterized and involves the ordered assembly of a number of general transcription factors (GTFs), all of which have been either cloned or purified to near homogeneity. In the human RNA polymerase II snRNA promoters, a single element, the proximal sequence element (PSE), is sufficient to direct basal levels of transcription in vitro. The PSE is recognized by the basal transcription complex SNAPc. SNAPc, which is not required for transcription from mRNA-type RNA polymerase II promoters such as the adenovirus type 2 major late (Ad2ML) promoter, is thought to recruit TATA binding protein (TBP) and nucleate the assembly of the snRNA transcription initiation complex, but little is known about which GTFs other than TBP are required. Here we show that the GTFs IIA, IIB, IIF, and IIE are required for efficient RNA polymerase II transcription from snRNA promoters. Thus, although the factors that recognize the core elements of RNA polymerase II mRNA and snRNA-type promoters differ, they mediate the recruitment of many common GTFs.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3225-3225
Author(s):  
Cecilia Grimaldi ◽  
Francesca Chiarini ◽  
Francesca Ricci ◽  
Pierluigi Tazzari ◽  
Michela Battistelli ◽  
...  

Abstract Abstract 3225 Over the past 20 years, survival rates of T-ALL patients have improved, mainly because of advances in chemotherapy protocols. Despite these improvements, we still need novel and less toxic treatment strategies targeting aberrantly activated signaling intermediates which increase proliferation, survival, and drug-resistance of T-ALL cells. One such intermediate is represented by the mammalian target of rapamycin (mTOR). mTOR exists as two complexes, referred to as mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2). Allosteric mTOR inhibitors (rapamycin and its analogs) mainly target mTORC1 and have displayed some promising effects in preclinical models of T-ALL. However, mTORC1 activity can be inhibited by activating AMP-dependent kinase (AMPK). AMPK activators include the antidiabetic drug, metformin. It is now emerging that metformin possesses antineoplastic activity in preclinical settings of solid tumors and its efficacy is being currently evaluated in cancer patients. Therefore, there is a strong rationale for further investigating the role of AMPK/mTORC1 signaling in malignant hematological disorders, as this pathway could represent a target for innovative treatments. Here, we have analyzed the therapeutic potential of metformin in T-ALL cell lines and pediatric patient lymphoblasts. We have used a panel of T-ALL cell lines including CEM-R [which overexpresses high levels of the membrane transporter, 170-kDa P-glycoprotein], Jurkat, and RPMI-8402 cells. Cell lines and fresh leukemia patients samples displayed mTORC1 activation as documented by the levels of Thr 37/46 p-4E-BP1 and Ser 235/236 p-S6 ribosomal protein. MTT assays demonstrated that metformin affected the viability of T-ALL cells. The IC50 for metformin at 48 h ranged from 1.6 to 5.6 mM in cell lines. When T-ALL patient samples were studied, metformin IC50 was 0.6–0.9 mM at 96 h. Remarkably, metformin targeted the side population (identified by flow cytometric analysis of Hoechst 33342 staining and ABCG2 expression) of T-ALL cell lines, which might correspond to leukemia initiating cells. Metformin induced apoptosis, as documented by western blot analysis with an antibody to caspase-8 and transmission electron microscopy analysis. Consistently with mTORC1 signaling inhibition, metformin caused autophagy, as demonstrated by transmission electron microscopy and western blot analysis with antibodies to beclin 1 and LC3B. Western blotting documented increased levels of Thr 172 p-AMPKα in CEM-R and RPMI8402 cells treated with metformin, indicating AMPKα activation. In contrast, no AMPKα activation was observed in Jurkat cells. Consistently with the activation of PKCζ/LKB1/AMPKα signaling, increased phosphorylation of Thr 410/403 p-PKCζ was detected in CEM-R and RPMI8402 cells. As a further proof of AMPKα activation by metformin, Ser 792 p-Raptor phosphorylation was seen in CEM-R and RPMI8402 cells. However, we detected decreased phosphorylation levels of Thr 37/46 p-4E-BP1, Ser 235/235 p-S6 ribosomal protein, Thr 389 p-p70S6K, and Ser 209 eIF4E in all the cell lines treated with metformin, implying inhibition of mTORC1 signaling. Decreased levels of Thr 37/46 p-4E-BP1 and Ser 235/235 p-S6 ribosomal protein were detected also in patient lymphoblasts. Interestingly, Ser 473 p-Akt levels decreased in Jurkat cells treated with metformin, suggesting that in this cell line, mTORC1 inhibition could be due to downregulation of IRS1/PI3K/Akt signaling, as recently demonstrated in breast cancer cell lines. Unlike rapamycin, metformin caused a marked inhibition of mRNA translation in T-ALL cell lines, as attested by a reduction in the incorporation of 3H-leucine and a shift from large to small polysomes. Our findings demonstrated that metformin was cytotoxic to T-ALL cell lines and patients lymphoblasts, activated AMPK through different mechanisms, downregulated mTORC1 signaling, and targeted mRNA translation more efficiently than rapamycin. The metformin concentrations which were cytotoxic to T-ALL cells are similar to the effective concentrations reported for solid tumors and could be obtained in human tissues and cells in vivo. The data could have a significant impact on our knowledge of both the relevance of AMPK/mTORC1 signaling as an innovative therapeutic target in T-ALL and the efficacy of metformin in this clinical setting. Disclosures: No relevant conflicts of interest to declare.


2010 ◽  
Vol 88 (6) ◽  
pp. 875-884 ◽  
Author(s):  
Michèle Amouyal

This review in two parts deals with the increasing number of processes known to be used by eukaryotic cells to protect gene expression from undesired genomic enhancer or chromatin effects, by means of the so-called insulators or barriers. The most advanced studies in this expanding field concern yeasts and Drosophila (this article) and the vertebrates (next article in this issue). Clearly, the cell makes use of every gene context to find the appropriate, economic, solution. Thus, besides the elements formerly identified and specifically dedicated to insulation, a number of unexpected elements are diverted from their usual function to structure the genome and enhancer action or to prevent heterochromatin spreading. They are, for instance, genes actively transcribed by RNA polymerase II or III, partial elements of these transcriptional machineries (stalled RNA polymerase II, normally required by genes that must respond quickly to stimuli, or TFIIIC bound at its B-box, normally required by RNA polymerase III for assembly of the transcription initiation complex at tRNA genes), or genomic sequences occupied by variants of standard histones, which, being rapidly and permanently replaced, impede heterochromatin formation.


Agriculture ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 81
Author(s):  
Taehoon Kim ◽  
Fábio Ometto Dias ◽  
Agustina Gentile ◽  
Marcelo Menossi ◽  
Kevin Begcy

RNA polymerase II is an essential multiprotein complex that transcribes thousands of genes, being a fundamental component of the transcription initiation complex. In eukaryotes, RNA polymerase II is formed by a 10-multisubunit conserved core complex, and two additional peripheral subunits, Rpb4 and Rpb7, form the Rpb4/7 subcomplex. Although transcription is vital for cell and organismal viability, little is known about the transcription initiation complex in sugarcane. An initial characterization of the sugarcane RNA polymerase subunit IV (ScRpb4) was performed. Our results demonstrate that ScRpb4 is evolutionarily conserved across kingdoms. At the molecular level, ScRpb4 expression was found in vegetative and reproductive tissues. Furthermore, the expression of ScRpb4 remained stable under various stress conditions, most likely to ensure a proper transcriptional response. Optimal conditions to express ScRpb4 in vitro for further studies were also identified. In this study, an initial characterization of the sugarcane polymerase II subunit IV is presented. Our results open the window to more specific experiments to study ScRpb4 function, for instance, crystal structure determination and pull-down assays as well as their function under biotic and abiotic stresses.


2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Thomas O. Krag ◽  
Sonja Holm-Yildiz ◽  
Nanna Witting ◽  
John Vissing

AbstractHypokalemic periodic paralysis is an autosomal dominant, rare disorder caused by variants in the genes for voltage-gated calcium channel CaV1.1 (CACNA1S) and NaV1.4 (SCN4A). Patients with hypokalemic periodic paralysis may suffer from periodic paralysis alone, periodic paralysis co-existing with permanent weakness or permanent weakness alone. Hypokalemic periodic paralysis has been known to be associated with vacuolar myopathy for decades, and that vacuoles are a universal feature regardless of phenotype. Hence, we wanted to investigate the nature and cause of the vacuoles. Fourteen patients with the p.R528H variation in the CACNA1S gene was included in the study. Histology, immunohistochemistry and transmission electron microscopy was used to assess general histopathology, ultrastructure and pattern of expression of proteins related to muscle fibres and autophagy. Western blotting and real-time PCR was used to determine the expression levels of proteins and mRNA of the proteins investigated in immunohistochemistry. Histology and transmission electron microscopy revealed heterogenous vacuoles containing glycogen, fibrils and autophagosomes. Immunohistochemistry demonstrated autophagosomes and endosomes arrested at the pre-lysosome fusion stage. Expression analysis showed a significant decrease in levels of proteins an mRNA involved in autophagy in patients, suggesting a systemic effect. However, activation level of the master regulator of autophagy gene transcription, TFEB, did not differ between patients and controls, suggesting competing control over autophagy gene transcription by nutritional status and calcium concentration, both controlling TFEB activity. The findings suggest that patients with hypokalemic periodic paralysis have disrupted autophagic processing that contribute to the vacuoles seen in these patients.


Methods ◽  
2017 ◽  
Vol 120 ◽  
pp. 115-124 ◽  
Author(s):  
Nicole Malkusch ◽  
Thilo Dörfler ◽  
Julia Nagy ◽  
Tobias Eilert ◽  
Jens Michaelis

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