Measuring In Vivo Supercoil Dynamics and Transcription Elongation Rates in Bacterial Chromosomes

2017 ◽  
pp. 17-27 ◽  
Author(s):  
N. Patrick Higgins
Keyword(s):  
Transcription Elongation ◽  
Bacterial Chromosomes

scholarly journals Transcription Elongation Activity of the Vaccinia Virus J3 Protein in Vivo Is Independent of Poly(A) Polymerase Stimulation

Virology ◽  
2000 ◽  
Vol 269 (2) ◽  
pp. 356-369 ◽  
Author(s):  
Ying Xiang ◽  
Donald R. Latner ◽  
Edward G. Niles ◽  
Richard C. Condit
Keyword(s):  
Vaccinia Virus ◽  
Transcription Elongation ◽  
Elongation Activity

scholarly journals Suppression of Factor-Dependent TranscriptionTermination by AntiterminatorRNA

2003 ◽  
Vol 185 (24) ◽  
pp. 7085-7091 ◽  
Author(s):  
Rodney A. King ◽  
Robert A. Weisberg
Keyword(s):  
Transcription Elongation ◽  
Intracellular Concentration ◽  
Elongation Complex ◽  
Rho Protein ◽  
Different Types ◽  
Presence And Absence ◽  
Nascent Transcripts

ABSTRACT Nascent transcripts of the phage HK022 put sites modify the transcription elongation complex so that it terminates less efficiently at intrinsic transcription terminators and accelerates through pause sites. We show here that the modification also suppresses termination in vivo at two factor-dependent terminators, one that depends on the bacterial Rho protein and a second that depends on the HK022-encoded Nun protein. Suppression was efficient when the termination factors were present at physiological levels, but an increase in the intracellular concentration of Nun increased termination both in the presence and absence of put. put-mediated antitermination thus shows no apparent terminator specificity, suggesting that put inhibits a step that is common to termination at the different types of terminator.

scholarly journals Requirement for Yeast RAD26, a Homolog of the HumanCSB Gene, in Elongation by RNA Polymerase II

2001 ◽  
Vol 21 (24) ◽  
pp. 8651-8656 ◽  
Author(s):  
Sung-Keun Lee ◽  
Sung-Lim Yu ◽  
Louise Prakash ◽  
Satya Prakash
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Rapid Synthesis ◽  
Developmental Defects ◽  
Developmental Abnormalities ◽  
Developmental Problems ◽  
Uv Lesions

ABSTRACT Mutations in the human CSB gene cause Cockayne syndrome (CS). In addition to increased photosensitivity, CS patients suffer from severe developmental abnormalities, including growth retardation and mental retardation. Whereas a deficiency in the preferential repair of UV lesions from the transcribed strand accounts for the increased photosensitivity of CS patients, the reason for developmental defects in these individuals has remained unclear. Here we provide in vivo evidence for a role of RAD26, the counterpart of the CSB gene in Saccharomyces cerevisiae, in transcription elongation by RNA polymerase II, and in addition we show that under conditions requiring rapid synthesis of new mRNAs, growth is considerably reduced in cells lackingRAD26. These findings implicate a role for CSB in transcription elongation, and they strongly suggest that impaired transcription elongation is the underlying cause of the developmental problems in CS patients.

scholarly journals FCP1, a Phosphatase Specific for the Heptapeptide Repeat of the Largest Subunit of RNA Polymerase II, Stimulates Transcription Elongation

2002 ◽  
Vol 22 (21) ◽  
pp. 7543-7552 ◽  
Author(s):  
Subhrangsu S. Mandal ◽  
Helen Cho ◽  
Sungjoon Kim ◽  
Kettly Cabane ◽  
Danny Reinberg
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Carboxy Terminal Domain ◽  
Transcription Factor Iif ◽  
Transcript Elongation ◽  
Rnap Ii ◽  
Carboxy Terminal

ABSTRACT FCP1, a phosphatase specific for the carboxy-terminal domain of RNA polymerase II (RNAP II), was found to stimulate transcript elongation by RNAP II in vitro and in vivo. This activity is independent of and distinct from the elongation-stimulatory activity associated with transcription factor IIF (TFIIF), and the elongation effects of TFIIF and FCP1 were found to be additive. Genetic experiments resulted in the isolation of several distinct fcp1 alleles. One of these alleles was found to suppress the slow-growth phenotype associated with either the reduction of intracellular nucleotide concentrations or the inhibition of other transcription elongation factors. Importantly, this allele of fcp1 was found to be lethal when combined individually with two mutations in the second-largest subunit of RNAP II, which had been shown previously to affect transcription elongation.

scholarly journals Coordination of Hpr1 and Ubiquitin Binding by the UBA Domain of the mRNA Export Factor Mex67

2007 ◽  
Vol 18 (7) ◽  
pp. 2561-2568 ◽  
Author(s):  
Maria Hobeika ◽  
Christoph Brockmann ◽  
Nahid Iglesias ◽  
Carole Gwizdek ◽  
David Neuhaus ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Conformational Change ◽  
Nuclear Export ◽  
Transcription Elongation ◽  
Mrna Export ◽  
Molecular Switch ◽  
Ubiquitin Binding ◽  
Uba Domain ◽  
Nuclear Export Receptor

The ubiquitin-associated (UBA) domain of the mRNA nuclear export receptor Mex67 helps in coordinating transcription elongation and nuclear export by interacting both with ubiquitin conjugates and specific targets, such as Hpr1, a component of the THO complex. Here, we analyzed substrate specificity and ubiquitin selectivity of the Mex67 UBA domain. UBA-Mex67 is formed by three helices arranged in a classical UBA fold plus a fourth helix, H4. Deletion or mutation of helix H4 strengthens the interaction between UBA-Mex67 and ubiquitin, but it decreases its affinity for Hpr1. Interaction with Hpr1 is required for Mex67 UBA domain to bind polyubiquitin, possibly by inducing an H4-dependent conformational change. In vivo, deletion of helix H4 reduces cotranscriptional recruitment of Mex67 on activated genes, and it also shows an mRNA export defect. Based on these results, we propose that H4 functions as a molecular switch that coordinates the interaction of Mex67 with ubiquitin bound to specific substrates, defines the selectivity of the Mex67 UBA domain for polyubiquitin, and prevents its binding to nonspecific substrates.

scholarly journals Functional Characterization of a New Member of the Cdk9 Family in Aspergillus nidulans

2010 ◽  
Vol 9 (12) ◽  
pp. 1901-1912 ◽  
Author(s):  
Friederike Bathe ◽  
Claudia Kempf ◽  
Stephen A. Osmani ◽  
Aysha H. Osmani ◽  
Sabrina Hettinger ◽  
...  
Keyword(s):  
Aspergillus Nidulans ◽  
Fluorescent Protein ◽  
Transcription Elongation ◽  
Functional Characterization ◽  
Asexual Development ◽  
Full Spectrum ◽  
Content Type ◽  
Essential Components

ABSTRACT Cdk9-like kinases in complex with T-type cyclins are essential components of the eukaryotic transcription elongation machinery. The full spectrum of Cdk9/cyclin T targets, as well as the specific consequences of phosphorylations, is still largely undefined. We identify and characterize here a Cdk9 kinase (PtkA) in the filamentous ascomycete Aspergillus nidulans. Deletion of ptkA had a lethal effect in later stages of vegetative growth and completely impeded asexual development. Overexpression of ptkA affected directionality of polarized growth and the initiation of new branching sites. A green fluorescent protein-tagged PtkA version localized inside the nucleus during interphase, supporting a role of PtkA in transcription elongation, as observed in other organisms. We also identified a putative cyclin T homolog, PchA, in the A. nidulans genome and confirmed its interaction with PtkA in vivo. Surprisingly, the Pcl-like cyclin PclA, previously described to be involved in asexual development, was also found to interact with PtkA, indicating a possible role of PtkA in linking transcriptional activity with development and/or morphogenesis in A. nidulans. This is the first report of a Cdk9 kinase interacting with a Pcl-like cyclin, revealing interesting new aspects about the involvement of this Cdk-subfamily in differential gene expression.

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