Overview of E. coli single stranded binding protein SSB and its cooperativity.

E. coli single stranded binding protein (Eco SSB) is encoded by ssb gene which consists of 534 bp in coding region. Product of ssb gene contains 177 amino acids with a molecular weight of 18,9 kDa. In solution, Eco SSB forms a tetramer as the active form (sometimes be viewed as a “dimer of dimers”). SSB is known to tightly bind single stranded DNA (ssDNA) with very high affinity and protects that ssDNA from nuclease, reannealing or secondary formation …  or keeps ssDNA intermediates, therefore involved in many cellular processes such as replication, recombination, repair. For example, during DNA replication, the double stranded separation by helicase and discontinuous replication of lagging strand generates a ssDNA bubble behind the replication fork, on lagging template. SSB covers this ssDNA to protect it from reannealing or nuclease digestion …. SSB can interact with other components of replication machinery. These interactions make SSB has some other important roles in DNA replication: primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, promotion of polymerase binding to the template, strand displacement activity of polymerase ….. In term of repair, Eco SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.

Eco SSB binds to ssDNA in a cooperative manner.  Some in vitro studies reveal that cooperativity of SSB is changed depending on the salt condition. In high salt condition (>0.2 M NaCl), ssDNA is coated by both dimers of the tetramer, therefore resulting an occluded site size of 65 nucleotides. That means 65 nucleotides requires 1 SSB tetramer. However, in the low salt concentration (<10 nM), ssDNA interacts with only one dimer, generating occluded site size of 35 nucleotides. In this case, cooperativity of SSB is highest and more SSB is needed for a particular template. In the intermediate salts (40-100 mM), the binding mode is 56. These numbers are very important for calculation of used SSB concentration for in vitro experiments.



Alexander G. Kozlov et al. SSB-DNA binding monitored by fluorescence intensity and anisotropy. Methods Mol Biol, 2012

Loic Hamon et al. High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein—DNA complexes. Nucleic Acids Res, 2007.

Aziz SANCAR et al. Sequences of the ssb gene and protein. Proc. NatL Acad. Sci. USA, 1981.
Ralph R. Meyer and Phyllis S. Laine. The Single-Stranded DNA-Binding Protein of Escherichia coli. Microbiological, 1990.



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