scholarly journals Structural basis of Q-dependent antitermination

2019 ◽  
Vol 116 (37) ◽  
pp. 18384-18390 ◽  
Author(s):  
Zhou Yin ◽  
Jason T. Kaelber ◽  
Richard H. Ebright
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Rna Polymerase ◽  
Structural Basis ◽  
Exit Channel ◽  
Late Genes ◽  
Q Protein

Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element (SDPE) to yield a Q-loading complex, and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. Here, we report high-resolution structures of 4 states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus, a “nozzle,” that narrows and extends the RNAP RNA-exit channel, extruding topologically linked single-stranded RNA and preventing the formation of pause and terminator hairpins.

scholarly journals Structural basis of Q-dependent antitermination

2019 ◽  
Author(s):  
Zhou Yin ◽  
Jason Kaelber ◽  
Richard H. Ebright
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Rna Polymerase ◽  
Structural Basis ◽  
Exit Channel ◽  
Late Genes ◽  
Q Protein ◽  
Rna Hairpins

AbstractLambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and an adjacent sigma-dependent pause element (SDPE) to yield a “Q-loading complex,” and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient “Q-loaded complex.” Here, we report high-resolution structures of four states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus--a “nozzle”--that narrows and extends the RNAP RNA-exit channel, extruding single-stranded RNA and preventing formation of pause and terminator hairpins.One Sentence SummaryQ forms a “nozzle” that narrows the RNA polymerase RNA-exit channel and extrudes ssRNA, preventing formation of RNA hairpins.

scholarly journals High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Zhijie Chen ◽  
Ronen Gabizon ◽  
Aidan I Brown ◽  
Antony Lee ◽  
Aixin Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Residence Time ◽  
Base Pair ◽  
High Accuracy ◽  
Control Of Gene Expression ◽  
Pol Ii ◽  
Crossing Time

Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression.

High resolution spot scan imaging of frozen, hydrated actin bundles with 400kV electrons

1992 ◽  
Vol 50 (1) ◽  
pp. 512-513
Author(s):  
J. Jakana ◽  
M.F. Schmid ◽  
P. Matsudaira ◽  
W. Chiu
Keyword(s):  
High Resolution ◽  
Binding Proteins ◽  
Actin Binding ◽  
Eukaryotic Cells ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Actin Bundle ◽  
Actin Bundles ◽  
3 Dimensional ◽  
Macromolecular Assembly

Actin is a protein found in all eukaryotic cells. In its polymerized form, the cells use it for motility, cytokinesis and for cytoskeletal support. An example of this latter class is the actin bundle in the acrosomal process from the Limulus sperm. The different functions actin performs seem to arise from its interaction with the actin binding proteins. A 3-dimensional structure of this macromolecular assembly is essential to provide a structural basis for understanding this interaction in relationship to its development and functions.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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