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Single-Strand DNA Binding Proteins01:03

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
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An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
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GapR binds DNA through dynamic opening of its tetrameric interface.

Qian Huang1, Bo Duan1, Xianzhi Dong2

  • 1Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.

Nucleic Acids Research
|August 7, 2020
PubMed
Summary

GapR, a key regulator of chromosome replication, forms a homotetramer, not a dimer. It binds DNA via an open conformation, then closes to encircle it, widening the minor groove of AT-rich DNA.

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Area of Science:

  • Microbiology
  • Structural Biology
  • Molecular Biology

Background:

  • GapR is an essential nucleoid-associated protein regulating chromosome replication in Caulobacter crescentus.
  • Previous studies reported GapR as a dimer, but its quaternary structure and DNA binding mechanism require further elucidation.

Purpose of the Study:

  • To determine the quaternary structure of free GapR.
  • To elucidate the mechanism of GapR-DNA interaction and its structural consequences.

Main Methods:

  • X-ray crystallography was used to determine the structure of GapR in complex with A-tract DNA.
  • Biophysical techniques were employed to analyze GapR's DNA binding affinity and specificity.

Main Results:

  • GapR exists as a homotetramer in solution, challenging previous dimer models.
  • Crystal structure revealed an open tetrameric conformation of GapR bound to DNA, distinct from a closed clamp conformation.
  • GapR binds AT-rich DNA nonselectively with high affinity (Kd ~12 nM) and GC-rich DNA with lower affinity (Kd ~120 nM).
  • GapR binding leads to widening of the DNA minor groove, particularly in AT-rich regions.

Conclusions:

  • GapR functions as a tetramer, initially binding DNA through an open conformation that rearranges to a closed, encircling state.
  • The protein's interaction with DNA involves minor groove widening, influencing DNA structure during replication regulation.