Structural Basis of Transcription Activation: The CAP-αCTD-DNA Complex

Benoff, B.; Yang, Huanwang; Lawson, Catherine L.; Parkinson, Gary N.; Liu, Jinsong; Blatter, Erich E.; Ebright, Richard H.; Berman, Helen M.

doi:10.1126/science.1076376

Cited by 235 publications

(268 citation statements)

References 46 publications

(40 reference statements)

Supporting

Mentioning

248

Contrasting

Order By: Relevance

“…Each subsite functions independently by recruiting one ␣CTD (11). The amino acid residues in ␣CTD that comprise the 265 determinant, including residues V264, R265, N268, N294, G296, K298, and S299, interact with UP element and A-tract sequences by contacting the DNA backbone, and R265 makes additional contacts with bases in the minor groove (4,32,43). These residues are the most important for rrnB P1 UP element utilization both in vivo and in vitro (13,35).…”

mentioning

confidence: 99%

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Husnain

Thomas

2008

J Bacteriol

View full text Add to dashboard Cite

The Escherichia coli guaB promoter (P guaB ) regulates the transcription of two genes, guaB and guaA, that are required for de novo synthesis of GMP, a precursor for the synthesis of guanine nucleoside triphosphates. The activity of P guaB is subject to growth rate-dependent control (GRDC). Here we show that the A؉T-rich sequence located between positions ؊59 and ؊38 relative to the guaB transcription start site stimulates transcription from P guaB ϳ8-to 10-fold and, in common with other UP elements, requires the C-terminal domain of the RNA polymerase ␣ subunit for activity. Like the rrnB P1 UP element, the P guaB UP element contains two independently acting subsites located at positions ؊59 to ؊47 and ؊46 to ؊38 and can stimulate transcription when placed upstream of the lacP1 promoter. We reveal a novel role for the P guaB UP element by demonstrating that it is required for GRDC. The involvement of the UP element in GRDC also requires the participation of sequences located at least 100 bp upstream of the guaB transcription start site. These sequences are required for down-regulation of P guaB activity at lower growth rates.Escherichia coli RNA polymerase (RNAP) is a multisubunit complex consisting of an ␣ subunit homodimer, single ␤, ␤Ј, and subunits, and one of several subunits (14). The ␣ subunit contains an N-terminal domain (␣NTD; residues 8 to 232) and a C-terminal domain (␣CTD; residues 249 to 329) (5, 21, 44). ␣NTD and ␣CTD are separated by a flexible linker that is at least 13 amino acids long (5,20,25). ␣CTD plays important roles in transcription activation by contacting a number of transcription factors (6, 18) or through interacting with an AϩT-rich DNA sequence referred to as the UP element (16).UP elements stimulate transcription by recruiting ␣CTD to DNA (32, 43). The best-studied UP element spans the region from Ϫ59 to Ϫ38 at the rrnB P1 promoter (16). The rrnB P1 UP element contains two domains, a ϳ9-bp proximal UP element subsite located at positions Ϫ46 to Ϫ38 and a ϳ13-bp distal UP element subsite located at positions Ϫ59 to Ϫ47. Each subsite functions independently by recruiting one ␣CTD (11). The amino acid residues in ␣CTD that comprise the 265 determinant, including residues V264, R265, N268, N294, G296, K298, and S299, interact with UP element and A-tract sequences by contacting the DNA backbone, and R265 makes additional contacts with bases in the minor groove (4, 32, 43). These residues are the most important for rrnB P1 UP element utilization both in vivo and in vitro (13, 35). In the absence of a strong distal UP element subsite, ␣CTD bound to a consensus or near-consensus proximal UP element subsite also makes productive contacts with region 4.2 of 70 that serve to stimulate transcription (7,35).The E. coli guaB promoter (P guaB ) regulates the transcription of two genes, guaB and guaA, which together constitute the guaBA operon. The guaB and guaA genes encode IMP dehydrogenase and GMP synthetase, respectively, and are required for the biosynthesis of GMP from IMP (22, 42). P guaB...

show abstract

mentioning

confidence: 99%

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Husnain

Thomas

2008

J Bacteriol

View full text Add to dashboard Cite

show abstract

“…The two segments are connected by a joint which allows random rotation within a certain range and following a certain probability distribution. As a result, the PDF of the end-to-end pose for the whole chain can be obtained as the convolution of three PDFs (8) where f 1 =f 1 (a,R,L 1 ) is the PDF of the pose of the frame of reference attached at the distal end of segment 1 relative to its own proximal end, f 2 =f 2 (a,R,L 2 ) is the PDF of the pose of the frame of reference attached at the distal end of segment 2 relative to its own proximal end, and f j is the PDF of the pose of the frame of reference attached at the proximal end of segment 2 relative to the distal end of segment 1. f j describes the junction between the two segments. Whereas f 1 (a,R,L 1 ) can be obtained by solving (3) with s=L 1 , and f 2 (a,R,L 2 ) can be obtained by solving (3) with s=L 2 , f j has the following form (9) The Dirac delta function in translation means that the two segments meet at a point rather than being translated in space relative to each other.…”

Section: General Ideamentioning

confidence: 99%

“…Letting g and h denote any group elements in SE(3), and letting f a (g) and f b (g) be two arbitrary functions defined on SE(3), the convolution on SE(3) is defined as 51 (10) where the little circle is the group multiplication operator for rigid-body motions. Equation (8) can be extended further to solve the multi-joint case by convolving more PDFs of involved segments and joints.…”

Section: General Ideamentioning

confidence: 99%

“…However, the Fourier transform for functions of SE (3)-valued argument provides a relatively easy way to compute (8). Applying the transform on both sides of (8), one obtains 51, 60 (11) It is a general property that the Fourier transform of a convolution of functions is the product of the Fourier transforms of those functions multiplied in the reverse order.…”

Section: General Ideamentioning

confidence: 99%

“…First discovered in the early 1980's 1 , intrinsically bent DNAs have been observed and studied experimentally [2][3][4][5][6][7][8] . Local structures, which are more complex than rigid bends, have also been observed from various experiments.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Conformational Statistics of Semiflexible Macromolecular Chains with Internal Joints

Chirikjian

2006

Macromolecules

View full text Add to dashboard Cite

Fluctuations in the bending angles at internal irregularities of DNA and RNA (such as symmetric loops, bulges, and nicks/gaps) have been observed from various experiments. However, little effort has been made to computationally predict and explain the statistical behavior of semiflexible chains with internal defects. In this paper, we describe the general structure of these macromolecular chains as inextensible elastic chains with one or more internal joints which have limited ranges of rotation, and propose a method to compute the probability density functions of the end-to-end pose of these macromolecular chains. Our method takes advantage of the operational properties of the non-commutative Fourier transform for the group of rigid-body motions in three-dimensional space, SE(3). Two representative types of joints, the hinge for planar rotation and the ball joint for spatial rotation, are discussed in detail. The proposed method applies to various stiffness models of semi-flexible chain-like macromolecules. Examples are calculated using the Kratky-Porod model with specified stiffness, angular fluctuation, and joint locations. Entropic effects associated with internal angular fluctuations of semi-flexible macromolecular chains with internal joints can be computed using this formulation. Our method also provides a potential tool to detect the existence of internal irregularities.

show abstract

Transcription: Initiation

Martin¹,

Mironova²

2008

Wiley Encyclopedia of Chemical Biology

View full text Add to dashboard Cite

Initiation of transcription is a complex process, requiring melting of the DNA duplex at a sequence‐defined location, de novo synthesis of an initial dinucleotide, polymerization/growth from that dinucleotide to a larger oligonucleotide in an extended RNA‐DNA hybrid, displacement and threading of the 5′ end of the RNA into an exit channel, and release of the initial promoter contacts. These events are necessarily driven energetically by growth of the RNA‐DNA hybrid. It has long been expected and is now becoming structurally clear that stress inherent in this transformation leads to instability during this phase and is a source of the abortive release of short RNA products that is characteristic of RNA polymerases. That apparently unrelated single and multisubunit RNA polymerases share extensive mechanistic (but not structural) homology, likely reflects the demands of the process.

show abstract

Structural Basis of Transcription Activation: The CAP-αCTD-DNA Complex

Cited by 235 publications

References 46 publications

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Conformational Statistics of Semiflexible Macromolecular Chains with Internal Joints

Transcription: Initiation

Contact Info

Product

Resources

About