How Proteins Search for Their Specific Sites on DNA: The Role of DNA Conformation

Hu, Tao; Grosberg, Alexander Y.; Shklovskiǐ, B. I.

doi:10.1529/biophysj.105.078162

Cited by 165 publications

(246 citation statements)

References 27 publications

(92 reference statements)

Supporting

Mentioning

236

Contrasting

Unclassified

Order By: Relevance

“…We also note that, although TF genes and their sites may not be close along DNA, they may be proximal in space because of the organization of DNA in the cell (4,30) or looping of DNA (31,32), thus opening a possibility of gene regulation by DNA conformation (33,34). DNA conformation may also play an important role in the search process (11) A B C Fig. 4.…”

Section: Discussionmentioning

confidence: 97%

How gene order is influenced by the biophysics of transcription regulation

Kolesov

Wunderlich²,

Laikova³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

170

185

View full text Add to dashboard Cite

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression.diffusion ͉ genetics ͉ genomics ͉ protein-DNA interactions ͉ spatial effects T he colocalization of prokaryotic transcription factor (TF) genes and their binding sites is known from the pioneering work of Jacob and Monod (1) on the lactose operon and has been shown to be widespread (2-4) and essential for the formation of regulatory motifs (5). Some have hypothesized that TF-binding site colocalization is advantageous, in part, because it could expedite a TF's search for its site (2, 5-7) (the rapid search hypothesis). In prokaryotes, this speed-up by colocalization is possible because transcription and translation are coupled spatially and temporally. Therefore, TFs are synthesized near their genes and can rapidly bind colocalized sites (Fig. 1A). The arrival time of a TF to its site ultimately controls the timing of gene regulation, whereas fluctuations in the arrival time can lead to bursts of gene activity and noise in gene regulation. The rapid search hypothesis suggests that colocalization is favorable because expediting TF arrival makes regulation faster and more reliable.Both experimentally (see ref.8 for an overview) and theoretically (9-13), many have studied the broader question: how can a TF find its cognate site on DNA among Ϸ10 7 decoy sites in a fraction of a minute while moving in the crowded environment of the cell and hampered by other DNA-bound proteins? The general model of the process includes 3D spatial diffusion of the TF through the cell volume and 1D sliding of a TF along DNA. According to this m...

show abstract

Section: Discussionmentioning

confidence: 97%

How gene order is influenced by the biophysics of transcription regulation

Kolesov

Wunderlich²,

Laikova³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

170

185

View full text Add to dashboard Cite

show abstract

“…Multistep target location involving initial association with nonspecific DNA and subsequent binding to the target is called ''facilitated diffusion.'' It is generally accepted that rapid target search in vivo is made possible through a combination of one-dimensional diffusion along DNA segments and threedimensional transfer among DNA segments (12,13,16); the work reported here concerns the one-dimensional process.…”

mentioning

confidence: 99%

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA

Blainey¹,

Oijen²,

Banerjee³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

442

613

View full text Add to dashboard Cite

“…A protein's search for the target site is thought to be accelerated by facilitated diffusion along nonspecific DNA (3)(4)(5)(6). Recent work has yielded considerable insight in the possible search strategies of sitespecific proteins (7)(8)(9)(10)(11)(12)(13)(14)(15). Assisted by DNA looping some proteins can, for instance, intermittently bind to two DNA segments simultaneously.…”

mentioning

confidence: 99%

How DNA coiling enhances target localization by proteins

Broek

Lomholt²,

Kalisch

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

187

196

View full text Add to dashboard Cite

Many genetic processes depend on proteins interacting with specific sequences on DNA. Despite the large excess of nonspecific DNA in the cell, proteins can locate their targets rapidly. After initial nonspecific binding, they are believed to find the target site by 1D diffusion (''sliding'') interspersed by 3D dissociation/reassociation, a process usually referred to as facilitated diffusion. The 3D events combine short intrasegmental ''hops'' along the DNA contour, intersegmental ''jumps'' between nearby DNA segments, and longer volume ''excursions.'' The impact of DNA conformation on the search pathway is, however, still unknown. Here, we show direct evidence that DNA coiling influences the specific association rate of EcoRV restriction enzymes. Using optical tweezers together with a fast buffer exchange system, we obtained association times of EcoRV on single DNA molecules as a function of DNA extension, separating intersegmental jumping from other search pathways. Depending on salt concentration, targeting rates almost double when the DNA conformation is changed from fully extended to a coiled configuration. Quantitative analysis by an extended facilitated diffusion model reveals that only a fraction of enzymes are ready to bind to DNA. Generalizing our results to the crowded environment of the cell we predict a major impact of intersegmental jumps on target localization speed on DNA.A n essential feature in biological processes on DNA is the ability of proteins to quickly locate specific DNA sequences in a vast surplus of nonspecific DNA (1, 2). A protein's search for the target site is thought to be accelerated by facilitated diffusion along nonspecific DNA (3-6). Recent work has yielded considerable insight in the possible search strategies of sitespecific proteins (7-15). Assisted by DNA looping some proteins can, for instance, intermittently bind to two DNA segments simultaneously. This way they can directly move from one to another chemically remote segment (16). This intersegmental transfer accelerates target finding on DNA because it assumes a constantly changing random configuration (11). Here, we demonstrate and quantify a similar mechanism, intersegmental jumping, for proteins with only one DNA-binding site.Little experimental work on facilitated diffusion is available. To date, most studies have been investigating DNA cleavage by restriction enzymes in bulk assays, measuring association times as a function of DNA length, or monitoring processivity on DNA constructs with two sites (7,(17)(18)(19)(20)(21). Although in these biochemical assays valuable information can be obtained, association rates of proteins to specific sites are difficult to measure, and the underlying kinetics of the target search mechanism are often obscured. Furthermore, it remains experimentally challenging to distinguish 1D and 3D search pathways. In previous singlemolecule assays only pure 1D protein search has been addressed (21-24). Here, we present single-molecule measurements of DNA cleavage by EcoRV on individual plasm...

show abstract

How Proteins Search for Their Specific Sites on DNA: The Role of DNA Conformation

Cited by 165 publications

References 27 publications

How gene order is influenced by the biophysics of transcription regulation

How gene order is influenced by the biophysics of transcription regulation

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA

How DNA coiling enhances target localization by proteins

Contact Info

Product

Resources

About