PROTEINS 2015* Intracellular and nuclear activity of a secreted macrophage metalloproteinase in viral infection is essential to invoke the IFN secretion by regulating gene transcription. (#11)
Proteases have both detrimental and beneficial roles in innate immunity and pathology. Moonlighting nuclear transcription roles for an extracellular secreted matrix metalloproteinase (MMP) are revealed for the first time. Using knockout mouse models we found that the secreted macrophage metalloproteinase, MMP12, translocates to the nucleus of virus-infected cells in trans. In the nucleus, MMP12 unexpectedly functions as a transcription factor and activates gene expression of IκBɑ upon binding the IκBα promoter, at a site we mapped to single nucleotide resolution. We found that IκBα was essential for secretion of IFNα. We rescued IκBα expression and IFNɑ secretion in Mmp12-/- cells by transfection or addition of recombinant MMP12 that translocates to the nucleus where it drives IκBα gene expression. Other protease-regulated genes during infection were also identified by ChIP-SEQ where transcription is repressed upon binding exon regions of these genes. By combining ChIP-SEQ with TAILS, a targeted N-terminomics procedure for identifying protease substrates by enrichment of the cleaved neo N-terminal peptides, we developed a proteogenomic approach to identify substrates whose expression is repressed at both the gene and protein levels by the protease. Hence, nuclear MMP12 down-regulates gene expression by binding target gene exons. Second, MMP12 mops-up the remaining substrate protein in the cytoplasm to rapidly deplete specific target proteins, a response which is essential for resistance to virus infection. Third, MMP12 clears secreted IFNα so we developed a new broad-spectrum antiviral drug targeting extracellular MMP12 to boost systemic IFNα levels and to also not cross cell membranes—thus sparing the beneficial nuclear activities of the protease. Thus, our proteogenomic approach identifies those substrates whose expression is regulated at both the genetic and protein level by a protease to rapidly deplete the protein from the system, that in viral infection is essential for the IFNα response and survival.
