<scp>T</scp>he IDL of <i>E. coli</i> SSB links ssDNA and protein binding by mediating protein–protein interactions

Bianco, Piero R.; Pottinger, Sasheen; Tan, Hui Yin; Nguyen-Duc, Trong; Rex, Kervin; Varshney, Umesh

doi:10.1002/pro.3072

Cited by 46 publications

(106 citation statements)

References 72 publications

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“…It is well known that a key element of the SSB protein is the OB‐fold (Raghunathan, Ricard, Lohman, & Waksman, ). This fold is responsible for binding both ssDNA and the linker domain of adjacent SSB tetramers thereby enabling cooperative interactions (Bianco et al, ; Savvides et al, ). Importantly, the OB‐fold is structurally almost identical to Src homology 3 (SH3) domains found in eukaryotes (Agrawal & Kishan, ).…”

Section: Discussionmentioning

confidence: 99%

“…The concentration of the purified proteins was determined at 280 nm using ε = 30,000 M ‐1 cm ‐1 . Histidine‐tagged SSB protein was purified as described previously (Bianco et al, ; Liu et al, ) .…”

Section: Methodsmentioning

confidence: 99%

“…SSB also interacts with an array of at least fourteen proteins that has been termed the SSB interactome (Costes, Lecointe, McGovern, Quevillon‐Cheruel, & Polard, ; Yu et al, ). These two seemingly disparate roles are intimately linked via the linker domain of the protein as explained below (Bianco et al, ).…”

Section: Introductionmentioning

confidence: 99%

“…The C-terminal domain of SSB can be further subdivided into two subdomains: a sequence of approximately 54 residues comprising residues 116-170, that is known as the linker and, the last eight residues which are known as the acidic tip (Kozlov et al, 2015;Shereda et al, 2008). The linker contains several structural elements critical to its function, including PXXP motifs (Bianco, 2017;Bianco et al, 2017;Tan et al, 2017). Critical to SSB function, the PXXP motifs in the linkers of one tetramer bind to the OB-fold(s) present in a nearby tetramer thereby facilitating cooperative ssDNA binding (Bianco, 2017;Bianco et al, 2017;Tan et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Super‐resolution imaging reveals changes in Escherichia coli SSB localization in response to DNA damage

Zhao

Liu

Wang³

et al. 2019

Genes to Cells

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The E. coli single‐stranded DNA‐binding protein (SSB) is essential to viability. It plays key roles in DNA metabolism where it binds to nascent single strands of DNA and to target proteins known as the SSB interactome. There are >2,000 tetramers of SSB per cell with 100–150 associated with the genome at any one time, either at DNA replication forks or at sites of repair. The remaining 1,900 tetramers could constantly diffuse throughout the cytosol or be associated with the inner membrane as observed for other DNA metabolic enzymes. To visualize SSB localization and to ascertain potential spatiotemporal changes in response to DNA damage, SSB‐GFP chimeras were visualized using a novel, super‐resolution microscope optimized for the study of prokaryotic cells. In the absence of DNA damage, SSB localizes to a small number of foci and the excess protein is associated with the inner membrane where it binds to the major phospholipids. Within five minutes following DNA damage, the vast majority of SSB disengages from the membrane and is found almost exclusively in the cell interior. Here, it is observed in a large number of foci, in discreet structures or, in diffuse form spread over the genome, thereby enabling repair events.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Super‐resolution imaging reveals changes in Escherichia coli SSB localization in response to DNA damage

Zhao

Liu

Wang³

et al. 2019

Genes to Cells

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“…5,6 These two seemingly disparate roles are intimately linked via a previously under-appreciated region of the protein known as the intrinsically disordered linker or IDL. 7 SSB exists as a homo-tetramer consisting of four, 18, 843 Dalton monomers. 8 Each subunit is composed of two domains: an N-terminal domain of approximately 116 residues that consists of an oligonucleotide/oligosaccharide binding fold (OB fold) and a C-terminal domain composed of the last 62 residues that extends outward from the core [ Fig.…”

Section: Introductionmentioning

confidence: 99%

The intrinsically disordered linker of E. coliSSB is critical for the release from single‐stranded DNA

et al. 2017

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The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, they have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target. In this study, they examine the role of the linker region in SSB function in a variety of DNA metabolic processes in vitro. Using the same linker mutants, the results show that in addition to association reactions (either DNA or protein), the IDL is critical for the release of SSB from DNA. This release can be under conditions of ssDNA competition or active displacement by a DNA helicase or recombinase. Consistent with their previous work these results indicate that SSB linker mutants are defective for SSB-SSB interactions, and when the IDL is removed a terminal SSB-DNA complex results. Formation of this complex inhibits downstream processing of DNA by helicases such as RecG or PriA as well as recombination, mediated by RecA. A model, based on the evidence herein, is presented to explain how the IDL acts in SSB function.

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SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork

Bianco

Lyubchenko

2017

Protein Science

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In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy. This translocation may be used to clear the fork of obstacles, prior to the initiation of fork regression.

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The IDL of E. coli SSB links ssDNA and protein binding by mediating protein–protein interactions

Cited by 46 publications

References 72 publications

Super‐resolution imaging reveals changes in Escherichia coli SSB localization in response to DNA damage

Super‐resolution imaging reveals changes in Escherichia coli SSB localization in response to DNA damage

The intrinsically disordered linker of E. coliSSB is critical for the release from single‐stranded DNA

SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork

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