Robust immune responses are essential for eliminating pathogens, but must be metered to avoid prolonged immune activation and potential host damage. Upon recognition of microbial DNA, the cytosolic DNA sensor cyclic GMP-AMP (cGAMP) synthetase, or cGAS, produces the second messenger cGAMP to initiate the STING pathway and subsequent interferon (IFN) production. We report that the direct interaction between cGAS and the Beclin-1 autophagy protein not only suppresses cGAMP synthesis to halt IFN production upon double stranded (ds)DNA stimulation or herpes simplex virus-1 infection, but also enhances autophagy-mediated degradation of cytosolic pathogen DNAs to prevent excessive cGAS activation and persistent immune stimulation. Specifically, this interaction releases Rubicon, a negative autophagy regulator, from the Beclin-1 complex, activating phosphatidylinositol 3-kinase class III activity and thereby inducing autophagy to remove cytosolic pathogen DNAs. Thus, the cGAS-Beclin-1 interaction shapes innate immune responses by regulating both cGAMP production and autophagy, resulting in well-balanced anti-microbial immune responses.

MicroRNAs (miRNAs) are potent RNA regulators of gene expression. Some viruses encode miRNAs, most of unknown function. The majority of viral miRNAs are not conserved, and whether any have conserved functions remains unclear. Here, we report that two human polyomaviruses associated with serious disease in immunocompromised individuals, JC virus and BK virus, encode miRNAs with the same function as that of the monkey polyomavirus simian virus 40 miRNAs. These miRNAs are expressed late during infection to autoregulate early gene expression. We show that the miRNAs generated from both arms of the pre-miRNA hairpin are active at directing the cleavage of the early mRNAs. This finding suggests that despite multiple differences in the miRNA seed regions, the primary target (the early mRNAs) and function (the downregulation of early gene expression) are evolutionarily conserved among the primate polyomavirus-encoded miRNAs. Furthermore, we show that these miRNAs are expressed in individuals diagnosed with polyomavirus-associated disease, suggesting their potential as targets for therapeutic intervention.MicroRNAs (miRNAs) are small, ϳ22-nucleotide RNA molecules that regulate gene expression (1). miRNAs bind to an mRNA and can repress translation or direct the cleavage of the target mRNA as part of the multiprotein RNA-induced silencing complex (RISC). The so-called seed region (nucleotides 2 to 8 of the 5Ј ends of miRNAs) plays an important role in target selection by RISC-bound miRNAs (4). Host-encoded miRNAs have been shown previously to play a role in processes relevant to viral infection, such as apoptosis and the adaptive and innate immune responses (12). Additionally, members of several virus families have been reported to encode miRNAs (3,5,15,17,18,20). Activities have been ascribed to a few such miRNAs; however, the functions of the majority of virus-encoded miRNAs remain poorly understood.We have shown previously that the monkey polyomavirus simian virus 40 (SV40) encodes a pre-miRNA late during infection that is processed into two miRNAs (23). Both SV40-encoded miRNAs function to downregulate the expression of the viral early genes by directing their RISC-mediated cleavage. The two human polyomaviruses JC virus (JCV) and BK virus (BKV) cause significant morbidity and mortality in immunosuppressed patients (2, 16). JCV is the causative agent of a fatal central nervous system demyelinating disease, progressive multifocal leukoencephalopathy (PML). BKV is the causative agent of polyomavirus-associated nephropathy in renal transplant patients. Currently, there are no drugs that are effective against polyomaviral infection. In this report, we now show that the human polyomaviruses BKV and JCV also encode miRNAs. Interestingly, results from fine-mapping studies show that the JCV and BKV miRNAs contain multiple differences in their seed sequences compared to the seed sequences of the SV40 miRNAs. Despite this finding, these miRNAs show similarities to the SV40 miRNAs in processing and share a conserved autoregulator...

STING is an endoplasmic reticulum (ER) signaling adaptor that is essential for the type I Interferon response to DNA pathogens. Aberrant activation of STING is linked to the pathology of autoimmune and autoinflammatory diseases. The rate-limiting step for the activation of STING is its translocation from the ER to the ER–Golgi intermediate compartment. Here we found that deficiency in the Ca 2+ sensor STIM1 caused spontaneous activation of STING and enhanced expression of type I interferons under resting conditions in mice and a patient suffering from combined immunodeficiency. Mechanistically, STIM1 associated with STING to retain it in the ER membrane, and co-expression of full-length or a STING-interacting fragment of STIM1 suppressed the function of dominant STING mutants that cause autoinflammatory diseases. Furthermore, deficiency in STIM1 strongly enhanced the expression of type I interferons after viral infection and prevented the lethality of infection with a DNA virus in vivo. This work delineates a STIM1–STING circuit that maintains the resting state of the STING pathway.

SUMMARY RNA interference (RNAi) is an established antiviral defense mechanism in plants and invertebrates. Whether RNAi serves a similar function in mammalian cells remains unresolved. We find that in some cell types, mammalian RNAi activity is reduced shortly after viral infection via poly ADP-ribosylation of the RNA induced silencing complex (RISC), a core component of RNAi. Well-established antiviral signaling pathways, including RIG-I/MAVS and RNAseL, contribute to inhibition of RISC. In the absence of virus infection, microRNAs repress interferon-stimulated genes (ISGs) associated with cell death and proliferation, thus maintaining homeostasis. Upon detection of intracellular pathogen-associated molecular patterns, RISC activity decreases, contributing to increased expression of ISGs. Our results suggest that unlike in lower eukaryotes, mammalian RISC is not antiviral in some contexts, but rather, RISC has been co-opted to negatively regulate toxic host antiviral effectors via microRNAs.

microRNAs (miRNAs) are post-transcriptional regulators of gene expression that play a role in viral infection. We have developed a method to identify viral-encoded miRNAs from viruses in which abundant amounts of infected material is limiting. We show that Merkel Cell Polyomavirus (MCV), a recently identified human virus associated with cancer, encodes a miRNA. This miRNA is expressed from the late strand, lies antisense to the early transcripts and negatively regulates expression of chimeric reporters containing a portion of the early transcripts. Interestingly, different viral isolates have sequence polymorphisms in the pre-miRNA region that result in amino acids substitutions but fully preserve the processing and activity of the miRNAs.