功能微生物生态系统组装综述：从分子线路到群落功能

图示信息：Figure 3 Illustrations for orthogonal transcription regulations based on different tools. (A) Orthogonal regulations of E. coli RNAP and Bacillus subtilis sigma factors without cr osstalk. (B) illustr ation for tr anslation-r epr essing ribor egulators. Tr anslation r egulation by the binding of ribosome binding site (RBS) and start codon and two single-stranded domains a ∗and b ∗. (C) Illustration for a biomolecular feedback controller. The htpG1 promoter drives the expression of CRISPR sgRNA, which in turn directs binding of dCas9 to target pBAD promoter to inhibit transcription of VioB–mCherry. (D) Muconic acid (MA) promotes the expression of the phosphoenolpyruvate metabolic node (EP module) and decreases the carbon flux into the TCA cycle via RNAi. (E) The DAPG-induced PhIF r epr essor was regulated using either the constitutive promoter (Pconst) or the TALEsp1 stabilized promoter. (F) Molecular implementation of tr anscription incoher ent-feedforw ar d-loop netw orks, in which the LacI is induced by IPTG; cI434, T7 RNAP, and sfGFP are the r epr essor, activ ator, and the output, r espectiv el y. used as DNA-binding regulators and are regarded as “gatek ee p- ers” for various

论文结果 / 观点：该图把群落互作落实到代谢物、电子或营养物交换，是理解共培养功能涌现的关键证据。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：fuae026.pdf，PDF 第 8 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 4. Illustrations for orthogonal translation regulations based on different tools. (A) Orthogonal function evolved for the wild type ribosome and fully orthogonal ribosome (Ribo-T) system. (B) Schematic overview of [4,5-d] pyrimidine-2,4-diamine (PPDA) responsive orthogonal riboswitch. (C) Illustration of the histamine-specific corresponding ribosome s witches . Histamine binding to aptamer disrupts the secondary structure of RNA and activates the translation state. (D) Techniques to engineer tRNA including aaRS identity elements, EF-Tu binding, EF-P binding, and four loops. (E) Sc hematic ov ervie w of the orthogonal pairs of ncAA, aaRS, and tRNA. ncAAs ar e r ecognized b y orthogonal aaRSs, loaded onto orthogonal tRN As. (F) A pipeline to identify orthogonal aaRS–tRNA pairs. First, the method of calculation or experiment was used to produce a series of candidate tRNAs, and then orthogonal tRN As w er e experimentall y confirmed. Subsequentl y, the activ e homologous synthases wer e scr eened and their orthogonality to eac h other was confirmed. Orthogonal protein regulations In addition to genetic circuits based on transcription and trans- lation le v els, ther e ar e man y

论文结果 / 观点：该图支撑“群落构建后必须验证功能”的观点，强调组学、示踪、功能测定或模型不能脱离实验验证。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：fuae026.pdf，PDF 第 10 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 5. Orthogonal regulatory strategies based on protein circuits. (A) Illustration of the CHOMP circuit. SOS activates Ras, causing it to bind RBD, r econstituting RasTEVP. TVMVP cleav a ge detac hes Casp3 and r educes its ability by membr ane-localized TEVP. (B) Sc heme of c hemicall y inducible split proteases with rapamycin based on a coiled-coils (CC) interaction module . T he complementary split fragments of the protease were fused to a domain pair, the pr oteol ytic acti vity was obtained after the ad dition of the inducer r a pamycin, and the leucine zipper was r emov ed to activ ate the lucifer ase r econstitution. (C) Sc hematic ov ervie w of the basic input of the pr otein cir cuit b y adjusting the binding str ength of the dimer. The inactiv ation operation was performed by separating the formed dimer through competitive binding, and the activation operation was performed by connecting two non-interacting monomers and recombining the fused split protein domains. (D) Schematic mechanism of multi-state biosensors . T he binding of the target and k e y allows the reconstitution of SmBiT and LgBiT for luciferase activity. (E) Illustration of the LOCKR system. The protein

论文结果 / 观点：该图支撑正文关于合成菌群设计、构建、验证或应用边界的核心论证。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：fuae026.pdf，PDF 第 11 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 7. Illustrations of the assembling of microbial ecosystems for bio-computing. (A) Diagram of the fragrance-programmable analog-to-digital converter with Boolean expression logic, including sampling-and-quantization module, gas-to-liquid transducer, and the digitizer module with signal amplifier. (B) Dia gr am of 7-str ain AND–XOR biocomputing circuit with thr ee inputs and four orthogonal c hannels , i.e . anhydr otetr acycline HCl (aTc), cuminic acid (Cuma), N-(3-Oxohexanoyl)-L-homoserine lactone (3OC6), and p-coumaroyl-HSL (pC). (C) Schematic diagram of the 7-strain digital display with four signal inputs, i.e. IPTG, N-(3-hydr oxytetr adecanoyl)-l-homoserine lactone (3OHC14), aTc, and 3OC6. (D) Sc hematic dia gr am of a QS-based perceptron network among two E. coli strains that based on the sending and receiving 3OC6 and 3OHC14 QS molecules. (Fig. 9 d). Ther efor e, differ ent micr obial ecosystems will provide us with important selections and strategies to face the major chal- lenges of environmental safety. As stated abo ve , the r a pid de v elopment of biotec hnology in synthetic biology has expanded the engineering ability of micro- bial ecosystems, which can effectiv

论文结果 / 观点：该图支撑正文关于合成菌群设计、构建、验证或应用边界的核心论证。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：fuae026.pdf，PDF 第 14 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 10. Micr obial inter actions design for differ ent synthetic micr obial consortia. (A) Inter action design of E. coli –S. cerevisiae consortium for production of oxygenated taxanes through the utilization of xylose and acetate. (B) Interaction design of the L. lactis C α-C β-Kp community in different pH conditions . T he pH-r esponse pr omoter dynamicall y r ealizes its switc hes fr om inactiv ation to activ ation with pH r eduction. (C) Inter action topology of a r oc k-pa per-scissors consortium. Eac h E. coli str ain could kill or be killed b y one of the other tw o strains b y producing its o wn to xin-antito xin pair and the toxin, such as the colicin E3, E, and V, against the next str ain. (D) Inter action dia gr am of thr ee- and four-strain consortia composed of different L. lactis strains. For example, ther e ar e commensalism r elationships among CmA, CmB, and CmBn, as well as the complex interaction consisting of the two commensalism strains (CmA and CmBn), a predation strain (PrB), and a cooperation strain (CoAg). some other r esearc hers . For example , r ecentl y, Hu et al. pr oposed that the behavior of microbial ecosystems can be predicted by mastering only t

论文结果 / 观点：该图支撑正文关于合成菌群设计、构建、验证或应用边界的核心论证。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：fuae026.pdf，PDF 第 19 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。