Innate Immune Sensing of Phages
噬菌体的先天免疫感应
While clearance by phagocytes is the ultimate fate of most phages in circulation, phages are internalized by a diverse set of eukaryotic cells via nonspecific uptake, receptor-mediated endocytosis, and uptake of bacteria-harboring prophages (77). While much of this literature involves tumor cell lines and phages engineered for biotechnology applications, uptake of natural (unmodified) phages is widespread and may proceed via similar routes. For example, E. coli phage T4 expresses a Lys-Gly-Asp motif on its capsid protein gp24 and was shown to interact with β3-integrin receptors on target cells (78). Other studies have implicated chondroitin sulfate proteoglycans in phage uptake (79). The filamentous E. coli phage M13 was reported to undergo receptor-mediated endocytosis via a diverse set of pathways depending on the cell line in question (80). For most phages, relevant receptors and mechanisms involved in cellular uptake are unknown.
虽然噬菌体被吞噬细胞清除是大多数噬菌体在血液循环中的最终归宿，但噬菌体也会通过非特异性摄取、受体介导的内吞作用以及摄取携带细菌的原噬菌体等方式被多种真核细胞内化（77）。虽然这些文献大多涉及肿瘤细胞系和为生物技术应用而设计的噬菌体，但天然（未修饰）噬菌体的摄取也很普遍，而且可能通过类似的途径进行。例如，大肠杆菌噬菌体 T4 在其噬菌体蛋白 gp24 上表达一个 Lys-Gly-Asp 矩阵，并被证明能与靶细胞上的β3-整合素受体相互作用（78）。其他研究表明，硫酸软骨素蛋白多糖与噬菌体的吸收有关 ( 79)。据报道，丝状大肠杆菌噬菌体 M13 可通过一系列不同的途径进行受体介导的内吞，具体取决于相关细胞系（80）。对于大多数噬菌体来说，参与细胞摄取的相关受体和机制尚不清楚。
Following internalization, phages are found within endosomal vesicles, cytoplasm, the nucleus, Golgi, and lysosomes, where they undergo degradation (79). Intracellular phages nonetheless retain some bioactivity against intracellular bacterial pathogens, as was recently shown for a case of Mycobacteria abscessus infection (81). It was also shown that phagocytosis can trigger prophage excision, allowing Listeria to escape from phagosomes (82). Along with cellular vesicles, phages can also enter the nucleus and produce both RNA and protein, as evidenced by research with phage DNA vaccines (83). The topic of intracellular phages is covered in depth in a recent review (84).
噬菌体内化后，会在内膜囊泡、细胞质、细胞核、高尔基体和溶酶体中被发现，并在那里被降解（79）。不过，细胞内噬菌体对细胞内细菌病原体仍有一定的生物活性，最近一例脓肿分枝杆菌感染病例就证明了这一点（81）。研究还表明，吞噬作用可引发噬菌体切除，使李斯特菌逃出吞噬体（82）。除了细胞囊泡，噬菌体还能进入细胞核并产生 RNA 和蛋白质，噬菌体 DNA 疫苗的研究证明了这一点 ( 83)。最近的一篇综述对细胞内噬菌体这一主题进行了深入探讨（84）。
Cellular uptake and transit position phages to be recognized by a number of cell-surface and intracellular pattern-recognition receptors (PRRs) (85). Pathways involving sensing of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and the induction of IFN responses are most commonly implicated (86).
噬菌体被细胞摄取和转运后，会被一些细胞表面和细胞内的模式识别受体（PRRs）识别（85）。涉及单链 DNA（ssDNA）和双链 DNA（dsDNA）感应以及诱导 IFN 反应的途径最常见（86）。
Several papers have identified a role for TLR9, an endosomal PRR, in phage recognition (49, 87). TLR9 recognizes unmethylated CpG motifs abundant in the DNA of phages as well as the bacteria that produce them (88, 89). TLR9 signals through the adaptor protein MyD88 and induces the expression of proinflammatory and antiviral cytokines (88). Recent research on phage sensing in the gut has also established a role for TLR9 in promoting inflammatory responses to phages. An oral cocktail of E. coli tailed phages led to significantly increased IFN-γ-producing CD4+ T cells, driven by DC sensing of phage DNA through TLR9 (49). However, the contribution of TLR9 to phage responses may be complex. Hashiguchi et al. (87) observed that MyD88−/− (the adaptor protein for all TLRs except TLR3) mice had minimal antibody responses in response to immunization with M13 phage, suggesting that TLR signaling is critical for antiphage adaptive immunity. However, TLR9−/− mice exhibited greatly increased IgG titers. While the authors posited that TLR9 may have a regulating effect on sensing of the M13 ssDNA genome, it remains unclear how this regulation might happen.
多篇论文已确定 TLR9（一种内体 PRR）在噬菌体识别中的作用 ( 49, 87)。TLR9 可识别噬菌体 DNA 中丰富的未甲基化 CpG 基序以及产生这些基序的细菌（88、89）。TLR9 通过适配蛋白 MyD88 发出信号，诱导促炎和抗病毒细胞因子的表达（88）。最近关于肠道噬菌体感应的研究也确定了 TLR9 在促进噬菌体炎症反应中的作用。大肠杆菌尾部噬菌体的口服鸡尾酒导致产生 IFN-γ 的 CD4 + T 细胞显著增加。T细胞，其驱动力是直流电通过TLR9感知噬菌体DNA ( 49)。然而，TLR9 对噬菌体反应的贡献可能很复杂。Hashiguchi 等人( 87) 观察到，MyD88 −/− （所有 TLR9 的适配蛋白）与噬菌体的反应有关。(除 TLR3 外，所有 TLR 的适配蛋白）小鼠对 M13 噬菌体免疫的抗体反应极小，这表明 TLR 信号传导对抗噬菌体适应性免疫至关重要。然而，TLR9 −/− 小鼠的 IgG 滴度大大增加。虽然作者认为 TLR9 可能对 M13 ssDNA 基因组的感应有调节作用，但目前还不清楚这种调节作用是如何发生的。
The stimulator of interferon genes (STING) pathway has been shown to be the major integrating axis for cytosolic dsDNA sensing (86). While there are indications that engineered phages reach the cytosol, there are no reports as of yet involving STING in phage sensing.
干扰素基因刺激器（STING）通路已被证明是细胞膜 dsDNA 感知的主要整合轴（86）。虽然有迹象表明工程噬菌体会进入细胞质，但目前还没有涉及 STING 在噬菌体感应中的作用的报道。
TLR3, an RNA sensor expressed within endosomes, has also been implicated in phage sensing (90). TLR3 is the only TLR that signals solely through the adaptor Toll/interleukin-1 receptor (IL-1R) resistance (TIR) domain–containing adapter-inducing IFN-β (TRIF) and induces robust induction of antiviral cytokines (88). Sweere et al. (90) reported that Pf, a filamentous P. aeruginosa–infecting phage, induced IFN-β production in DCs in a TLR3- and TRIF-dependent manner. Phage-derived RNA production within eukaryotic cells was demonstrated as the stimulus for this RNA-sensing receptor, although it is not yet understood how Pf is able to initiate transcription in a mammalian cell. This was not the first report of phage genome transcription in a eukaryotic system (91, 92), and phage DNA vaccines must make RNA in order to make protein (83).
TLR3 是一种在内质体中表达的 RNA 传感器，也与噬菌体感应有关 ( 90)。TLR3 是唯一一种仅通过含适配器诱导 IFN-β （TRIF）的 Toll/白细胞介素-1（IL-1R）受体（TIR）抗性（TIR）结构域发出信号的 TLR，并能诱导抗病毒细胞因子（88）。Sweere 等人（90）报道了一种丝状绿脓杆菌感染噬菌体 Pf 以 TLR3 和 TRIF 依赖性方式诱导直流细胞产生 IFN-β。噬菌体在真核细胞内产生的 RNA 被证明是这种 RNA 感知受体的刺激物，但目前还不清楚 Pf 是如何在哺乳动物细胞内启动转录的。这并不是真核系统中噬菌体基因组转录的首次报道（91、92），噬菌体 DNA 疫苗必须产生 RNA 才能产生蛋白质（83）。
Nonetheless, much remains unknown about bacterial uptake by mammalian cells. It is unclear whether individual phages are tropic for particular cell types. It is also unclear how phages move within a cell.
然而，哺乳动物细胞对细菌的吸收仍有许多未知之处。目前还不清楚单个噬菌体是否对特定类型的细胞具有趋性。噬菌体如何在细胞内移动也不清楚。