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The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex.

Stratmann SA, Morrone SR, van Oijen AM, Sohn J - Elife (2015)

Bottom Line: However, the molecular mechanisms underlying distinction between foreign DNA and host genomic material inside the nucleus are not understood.We also demonstrate that nucleosomes represent barriers that prevent IFI16 from targeting host DNA by directly interfering with these one-dimensional movements.This unique scanning-assisted assembly mechanism allows IFI16 to distinguish friend from foe and assemble into oligomers efficiently and selectively on foreign DNA.

View Article: PubMed Central - PubMed

Affiliation: University of Groningen, Groningen, Netherlands.

ABSTRACT
The ability to recognize foreign double-stranded (ds)DNA of pathogenic origin in the intracellular environment is an essential defense mechanism of the human innate immune system. However, the molecular mechanisms underlying distinction between foreign DNA and host genomic material inside the nucleus are not understood. By combining biochemical assays and single-molecule techniques, we show that the nuclear innate immune sensor IFI16 one-dimensionally tracks long stretches of exposed foreign dsDNA to assemble into supramolecular signaling platforms. We also demonstrate that nucleosomes represent barriers that prevent IFI16 from targeting host DNA by directly interfering with these one-dimensional movements. This unique scanning-assisted assembly mechanism allows IFI16 to distinguish friend from foe and assemble into oligomers efficiently and selectively on foreign DNA.

No MeSH data available.


Related in: MedlinePlus

FRET assembly assays using 25 nM donor and acceptor labeled IFI16 compared to 50 nM in Figure 1B.Shown is a representative of three experiments, and the calculated rates are listed in Supplementary file 1A.DOI:http://dx.doi.org/10.7554/eLife.11721.004
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fig1s1: FRET assembly assays using 25 nM donor and acceptor labeled IFI16 compared to 50 nM in Figure 1B.Shown is a representative of three experiments, and the calculated rates are listed in Supplementary file 1A.DOI:http://dx.doi.org/10.7554/eLife.11721.004

Mentions: (A) Top: IFI16 is composed of three functional domains flanked by unstructured linkers, namely one pyrin domain (PYD) and two dsDNA-binding Hin domains (HinA and HinB; Hin: hematopoietic interferon-inducible nuclear antigen). Bottom: IFI16 detects foreign dsDNA from invading pathogens in both the host nucleus and cytoplasm. (B) Top: a cartoon scheme for FRET experiments. The two differentially colored ovals represent fluorescently (Dylight-550 and Dylight-650) labeled IFI16. Bottom: The time-dependent changes in the emission ratio between FRET donor and acceptor labeled IFI16 (50 nM) were monitored at 33 µg/ml of each dsDNA (e.g. sixfold higher than the dissociation constant for 39-bp dsDNA [Morrone et al., 2014]). Lines are fits to a first-order exponential equation (see Figure 1—figure supplement 1 for 25 nM protein). All shown representative experiments were performed at least three times. (C) A plot of observed assembly rates (kassms) vs. dsDNA-sizes (see also Figure 1—figure supplement 1). (D) 1D-diffusion assisted assembly mechanism can explain the observed assembly profile of IFI16. 1. At the same mass-concentrations, the number of individual dsDNA fragments present in each assay is inversely proportional to the length of dsDNA. 2. Individual IFI16 molecules initially bind dsDNA at random positions and diffuse one-dimensionally while searching for other respective protomers; the number of IFI16 residing on the same dsDNA fragment should be proportional to the length of dsDNA (e.g. there are four times more individual 150-bp fragments than 600-bp fragments) 3. IFI16 fails to assemble into an oligomer on dsDNA shorter than 60 bp (indicated by a red arrow pointing left). The saturating rates can be explained if the final FRET signals arise from formation of distinct optimal oligomers.


The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex.

Stratmann SA, Morrone SR, van Oijen AM, Sohn J - Elife (2015)

FRET assembly assays using 25 nM donor and acceptor labeled IFI16 compared to 50 nM in Figure 1B.Shown is a representative of three experiments, and the calculated rates are listed in Supplementary file 1A.DOI:http://dx.doi.org/10.7554/eLife.11721.004
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829420&req=5

fig1s1: FRET assembly assays using 25 nM donor and acceptor labeled IFI16 compared to 50 nM in Figure 1B.Shown is a representative of three experiments, and the calculated rates are listed in Supplementary file 1A.DOI:http://dx.doi.org/10.7554/eLife.11721.004
Mentions: (A) Top: IFI16 is composed of three functional domains flanked by unstructured linkers, namely one pyrin domain (PYD) and two dsDNA-binding Hin domains (HinA and HinB; Hin: hematopoietic interferon-inducible nuclear antigen). Bottom: IFI16 detects foreign dsDNA from invading pathogens in both the host nucleus and cytoplasm. (B) Top: a cartoon scheme for FRET experiments. The two differentially colored ovals represent fluorescently (Dylight-550 and Dylight-650) labeled IFI16. Bottom: The time-dependent changes in the emission ratio between FRET donor and acceptor labeled IFI16 (50 nM) were monitored at 33 µg/ml of each dsDNA (e.g. sixfold higher than the dissociation constant for 39-bp dsDNA [Morrone et al., 2014]). Lines are fits to a first-order exponential equation (see Figure 1—figure supplement 1 for 25 nM protein). All shown representative experiments were performed at least three times. (C) A plot of observed assembly rates (kassms) vs. dsDNA-sizes (see also Figure 1—figure supplement 1). (D) 1D-diffusion assisted assembly mechanism can explain the observed assembly profile of IFI16. 1. At the same mass-concentrations, the number of individual dsDNA fragments present in each assay is inversely proportional to the length of dsDNA. 2. Individual IFI16 molecules initially bind dsDNA at random positions and diffuse one-dimensionally while searching for other respective protomers; the number of IFI16 residing on the same dsDNA fragment should be proportional to the length of dsDNA (e.g. there are four times more individual 150-bp fragments than 600-bp fragments) 3. IFI16 fails to assemble into an oligomer on dsDNA shorter than 60 bp (indicated by a red arrow pointing left). The saturating rates can be explained if the final FRET signals arise from formation of distinct optimal oligomers.

Bottom Line: However, the molecular mechanisms underlying distinction between foreign DNA and host genomic material inside the nucleus are not understood.We also demonstrate that nucleosomes represent barriers that prevent IFI16 from targeting host DNA by directly interfering with these one-dimensional movements.This unique scanning-assisted assembly mechanism allows IFI16 to distinguish friend from foe and assemble into oligomers efficiently and selectively on foreign DNA.

View Article: PubMed Central - PubMed

Affiliation: University of Groningen, Groningen, Netherlands.

ABSTRACT
The ability to recognize foreign double-stranded (ds)DNA of pathogenic origin in the intracellular environment is an essential defense mechanism of the human innate immune system. However, the molecular mechanisms underlying distinction between foreign DNA and host genomic material inside the nucleus are not understood. By combining biochemical assays and single-molecule techniques, we show that the nuclear innate immune sensor IFI16 one-dimensionally tracks long stretches of exposed foreign dsDNA to assemble into supramolecular signaling platforms. We also demonstrate that nucleosomes represent barriers that prevent IFI16 from targeting host DNA by directly interfering with these one-dimensional movements. This unique scanning-assisted assembly mechanism allows IFI16 to distinguish friend from foe and assemble into oligomers efficiently and selectively on foreign DNA.

No MeSH data available.


Related in: MedlinePlus