XAF1 prevents hyperproduction of type I interferon upon viral infection by targeting IRF7Liu, Bao‐qin; Liu, Rong‐bei; Li, Wen‐ping; Mao, Xin‐tao; Li, Yi‐ning; Huang, Tao; Wang, Hao‐li; Chen, Hao‐tian; Zhong, Jiang‐yan; Yang, Bing; Chai, Ren‐jie; Cao, Qian; Jin, Jin; Li, Yi‐yuan
doi: 10.15252/embr.202255387pmid: 36394357
Interferon regulatory factor (IRF) 3 and IRF7 are master regulators of type I interferon (IFN‐I)‐dependent antiviral innate immunity. Upon viral infection, a positive feedback loop is formed, wherein IRF7 promotes further induction of IFN‐I in the later stage. Thus, it is critical to maintain a suitably low level of IRF7 to avoid the hyperproduction of IFN‐I. In this study, we find that early expression of IFN‐I‐dependent STAT1 promotes the expression of XAF1 and that XAF1 is associated specifically with IRF7 and inhibits the activity of XIAP. XAF1‐knockout and XIAP‐transgenic mice display resistance to viral infection, and this resistance is accompanied by increases in IFN‐I production and IRF7 stability. Mechanistically, we find that the XAF1‐XIAP axis controls the activity of KLHL22, an adaptor of the BTB‐CUL3‐RBX1 E3 ligase complex through a ubiquitin‐dependent pathway. CUL3‐KLHL22 directly targets IRF7 and catalyzes its K48‐linked ubiquitination and proteasomal degradation. These findings reveal unexpected functions of the XAF1‐XIAP axis and KLHL22 in the regulation of IRF7 stability and highlight an important target for antiviral innate immunity.
The plant FYVE domain‐containing protein FREE1 associates with microprocessor components to repress miRNA biogenesisLi, Hongbo; Li, Tingting; Li, Yingzhu; Bai, Haiyan; Dai, Yanghuan; Liao, Yanglan; Wei, Juan; Shen, Wenjin; Zheng, Binglian; Zhang, Zhonghui; Gao, Caiji
doi: 10.15252/embr.202255037pmid: 36373807
FYVE domain protein required for endosomal sorting 1 (FREE1), originally identified as a plant‐specific component of the endosomal sorting complex required for transport (ESCRT) machinery, plays diverse roles either in endosomal sorting in the cytoplasm or in transcriptional regulation of abscisic acid signaling in the nucleus. However, to date, a role for FREE1 or other ESCRT components in the regulation of plant miRNA biology has not been discovered. Here, we demonstrate a nuclear function of FREE1 as a cofactor in miRNA biogenesis in plants. FREE1 directly interacts with the plant core microprocessor component CPL1 in nuclear bodies and disturbs the association between HYL1, SE and CPL1. Inactivation of FREE1 in the nucleus increases the binding affinity between HYL1, SE, and CPL1 and causes a transition of HYL1 from the inactive hyperphosphorylated version to the active hypophosphorylated form, thereby promoting miRNA biogenesis. Our results suggest that FREE1 has evolved as a negative regulator of miRNA biogenesis and provides evidence for a link between FYVE domain‐containing proteins and miRNA biogenesis in plants.
Sphingosine‐1‐phosphate controls endothelial sphingolipid homeostasis via ORMDLSasset, Linda; Chowdhury, Kamrul H; Manzo, Onorina L; Rubinelli, Luisa; Konrad, Csaba; Maschek, J Alan; Manfredi, Giovanni; Holland, William L; Di Lorenzo, Annarita
doi: 10.15252/embr.202254689pmid: 36408842
Disruption of sphingolipid homeostasis and signaling has been implicated in diabetes, cancer, cardiometabolic, and neurodegenerative disorders. Yet, mechanisms governing cellular sensing and regulation of sphingolipid homeostasis remain largely unknown. In yeast, serine palmitoyltransferase, catalyzing the first and rate‐limiting step of sphingolipid de novo biosynthesis, is negatively regulated by Orm1 and 2. Lowering sphingolipids triggers Orms phosphorylation, upregulation of serine palmitoyltransferase activity and sphingolipid de novo biosynthesis. However, mammalian orthologs ORMDLs lack the N‐terminus hosting the phosphosites. Thus, which sphingolipid(s) are sensed by the cells, and mechanisms of homeostasis remain largely unknown. Here, we identify sphingosine‐1‐phosphate (S1P) as key sphingolipid sensed by cells via S1PRs to maintain homeostasis. The increase in S1P‐S1PR signaling stabilizes ORMDLs, restraining SPT activity. Mechanistically, the hydroxylation of ORMDLs at Pro137 allows a constitutive degradation of ORMDLs via ubiquitin‐proteasome pathway, preserving SPT activity. Disrupting S1PR/ORMDL axis results in ceramide accrual, mitochondrial dysfunction, impaired signal transduction, all underlying endothelial dysfunction, early event in the onset of cardio‐ and cerebrovascular diseases. Our discovery may provide the molecular basis for therapeutic intervention restoring sphingolipid homeostasis.
Rassf7a promotes spinal cord regeneration and controls spindle orientation in neural progenitor cellsZhu, Panpan; Zheng, Pengfei; Kong, Xinlong; Wang, Shuo; Cao, Muqing; Zhao, Chengtian
doi: 10.15252/embr.202254984pmid: 36408859
Spinal cord injury (SCI) can cause long‐lasting disability in mammals due to the lack of axonal regrowth together with the inability to reinitiate spinal neurogenesis at the injury site. Deciphering the mechanisms that regulate the proliferation and differentiation of neural progenitor cells is critical for understanding spinal neurogenesis after injury. Compared with mammals, zebrafish show a remarkable capability of spinal cord regeneration. Here, we show that Rassf7a, a member of the Ras‐association domain family, promotes spinal cord regeneration after injury. Zebrafish larvae harboring a rassf7a mutation show spinal cord regeneration and spinal neurogenesis defects. Live imaging shows abnormal asymmetric neurogenic divisions and spindle orientation defects in mutant neural progenitor cells. In line with this, the expression of rassf7a is enriched in neural progenitor cells. Subcellular analysis shows that Rassf7a localizes to the centrosome and is essential for cell cycle progression. Our data indicate a role for Rassf7a in modulating spindle orientation and the proliferation of neural progenitor cells after spinal cord injury.
Time required for commitment to T cell proliferation depends on TCR affinity and cytokine responseWu, Liang‐zhe; Balyan, Renu; Brzostek, Joanna; Zhao, Xiang; Gascoigne, Nicholas R J
doi: 10.15252/embr.202254969pmid: 36327141
T cell activation and effector functions are determined by the affinity of the interaction between T cell receptor (TCR) and its antigenic peptide MHC (pMHC) ligand. A better understanding of the quantitative aspects of TCR‐pMHC affinity‐dependent T cell activation is critical for the development of new immunotherapeutic strategies. However, the role of TCR‐pMHC affinity in regulating the kinetics of CD8+ T cell commitment to proliferation and differentiation is unknown. Here, we show that the stronger the TCR‐pMHC affinity, the shorter the time of T cell‐APC co‐culture required to commit CD8+ T cells to proliferation. The time threshold for T cell cytokine production is much lower than that for cell proliferation. There is a strong correlation between affinity‐dependent differences in AKT phosphorylation and T cell proliferation. The cytokine IL‐15 increases the poor proliferation of T cells stimulated with low affinity pMHC, suggesting that pro‐inflammatory cytokines can override the affinity‐dependent features of T cell proliferation.
Nuclease‐independent functions of RAG1 direct distinct DNA damage responses in B cellsJohnston, Rachel; Mathias, Brendan; Crowley, Stephanie J; Schmidt, Haley A; White, Lynn S; Mosammaparast, Nima; Green, Abby M; Bednarski, Jeffrey J
doi: 10.15252/embr.202255429pmid: 36382770
Developing B cells generate DNA double‐stranded breaks (DSBs) to assemble immunoglobulin receptor (Ig) genes necessary for the expression of a mature B cell receptor. These physiologic DSBs are made by the RAG endonuclease, which is comprised of the RAG1 and RAG2 proteins. In pre‐B cells, RAG‐mediated DSBs activate the ATM kinase to coordinate canonical and non‐canonical DNA damage responses (DDR) that trigger DSB repair and B cell developmental signals, respectively. Whether this broad cellular response is distinctive to RAG DSBs is poorly understood. To delineate the factors that direct DDR signaling in B cells, we express a tetracycline‐inducible Cas9 nuclease in Rag1‐deficient pre‐B cells. Both RAG‐ and Cas9‐mediated DSBs at Ig genes activate canonical DDR. In contrast, RAG DSBs, but not Cas9 DSBs, induce the non‐canonical DDR‐dependent developmental program. This unique response to RAG DSBs is, in part, regulated by non‐core regions of RAG1. Thus, B cells trigger distinct cellular responses to RAG DSBs through unique properties of the RAG endonuclease that promotes activation of B cell developmental programs.
Retrotransposon insertions associated with risk of neurologic and psychiatric diseasesAhn, Hyo Won; Worman, Zelia F; Lechsinska, Arianna; Payer, Lindsay M; Wang, Tongguang; Malik, Nasir; Li, Wenxue; Burns, Kathleen H; Nath, Avindra; Levin, Henry L
doi: 10.15252/embr.202255197pmid: 36367221
Transposable elements (TEs) are active in neuronal cells raising the question whether TE insertions contribute to risk of neuropsychiatric disease. While genome‐wide association studies (GWAS) serve as a tool to discover genetic loci associated with neuropsychiatric diseases, unfortunately GWAS do not directly detect structural variants such as TEs. To examine the role of TEs in psychiatric and neurologic disease, we evaluated 17,000 polymorphic TEs and find 76 are in linkage disequilibrium with disease haplotypes (P < 10−6) defined by GWAS. From these 76 polymorphic TEs, we identify potentially causal candidates based on having insertions in genomic regions of regulatory chromatin and on having associations with altered gene expression in brain tissues. We show that lead candidate insertions have regulatory effects on gene expression in human neural stem cells altering the activity of a minimal promoter. Taken together, we identify 10 polymorphic TE insertions that are potential candidates on par with other variants for having a causal role in neurologic and psychiatric disorders.