工程化核酶介导的RNA信息记录技术解析微生物群落中的水平基因转移

孙艳鑫; 王世龙; 俞胜男; 江高飞; 韦中

doi:10.12211/2096-8280.2026-064

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工程化核酶介导的RNA信息记录技术解析微生物群落中的水平基因转移

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- 工程化核酶介导的RNA信息记录技术解析微生物群落中的水平基因转移
- Ribozyme-enabled RNA recording for analyzing mobile genetic element-host associations in microbial communities
- 合成生物学 2026年页码：1-8
- 作者机构：
  
  南京农业大学资源与环境科学学院，江苏南京 210095
- 作者简介：
  
  孙艳鑫（2001—），女，在读博士。研究方向为铁载体与根际健康。
  江高飞（1988—），男，教授，博士生导师。长期从事土壤生物健康培育研究，核心方向包括：土壤致病菌和耐药基因的环境风险过程与消减技术、人工智能与土壤微生物生态学等。
- 基金信息：
  
  国家自然科学基金(42477122;42325704);江苏省自然科学基金(BK20230102)
- DOI：10.12211/2096-8280.2026-064
  中图分类号： Q81
- 收稿：2026-07-20，
  
  修回：2026-09-07，
  
  网络首发：2026-09-09，
- 稿件说明：
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孙艳鑫，王世龙，俞胜男，江高飞，韦中. 工程化核酶介导的RNA信息记录技术解析微生物群落中的水平基因转移［J］. 合成生物学， 2026， 7. DOI： 10.12211/2096-8280.2026-064

SUN Yanxin， WANG Shilong， YU Shengnan， JIANG Gaofei， WEI Zhong. Ribozyme-enabled RNA recording for analyzing mobile genetic element–host associations in microbial communities［J］. Synthetic Biology Journal， 2026， 7. DOI： 10.12211/2096-8280.2026-064
孙艳鑫，王世龙，俞胜男，江高飞，韦中. 工程化核酶介导的RNA信息记录技术解析微生物群落中的水平基因转移［J］. 合成生物学， 2026， 7. DOI： 10.12211/2096-8280.2026-064 DOI：

SUN Yanxin， WANG Shilong， YU Shengnan， JIANG Gaofei， WEI Zhong. Ribozyme-enabled RNA recording for analyzing mobile genetic element–host associations in microbial communities［J］. Synthetic Biology Journal， 2026， 7. DOI： 10.12211/2096-8280.2026-064 DOI：

摘要

水平基因转移是微生物群落遗传信息交换和功能演化的重要驱动力，在微生物适应、抗生素耐药性传播以及环境生物安全评价中发挥重要作用。然而，在复杂环境微生物群落中，确定移动遗传元件的受体宿主及其宿主分布模式仍面临诸多技术挑战。传统培养方法、宏基因组测序以及空间关联技术能够提供遗传元件传播特征或群落遗传背景信息，但受到宿主可培养性限制、遗传元件—宿主关联缺失以及关联结果解释复杂等因素影响，难以全面解析非培养微生物体系中的遗传元件宿主范围。近年来，基于工程化核酶的信息记录技术——RNA可寻址修饰（RNA-addressable modification， RAM）为鉴定水平基因转移相关遗传元件携带状态及宿主关联模式提供了新的技术路径。该技术利用工程化I型内含子核酶介导RNA信息写入，将移动遗传元件编码的RNA条形码信息与宿主16S rRNA信息建立分子关联，从而将难以直接观测的遗传元件—宿主关联状态转化为可检测的分子记录。已有研究表明，RAM能够应用于质粒接合和噬菌体转导体系，并揭示不同移动遗传元件在环境微生物群落中的宿主分布差异，展示了其在复杂微生物群落遗传元件宿主范围分析中的应用潜力。本文围绕RAM的信息记录机制、微生物群落水平基因转移研究中的应用价值及其能力边界进行评述，并进一步讨论其与现有HGT研究方法之间的互补关系。本文认为，RAM的核心意义并不在于替代传统HGT检测策略，而在于改变遗传元件—宿主关系的信息获取方式，使部分过去依赖序列关联、空间关联或培养验证推断的信息转化为可记录、可读取的分子证据。需要指出的是，RAM记录的是特定时间尺度下遗传元件与宿主形成的关联状态，而非完整的水平基因转移传播过程。未来，通过优化工程化核酶性能、融合累积型信息记录体系以及拓展生态应用场景，RAM有望进一步发展为解析微生物群落中遗传元件分布模式及宿主关联特征的重要分子记录平台。

Abstract

Horizontal gene transfer (HGT) is a major driver of genetic information exchange and functional evolution in microbial communities

contributing to microbial adaptation

antibiotic resistance dissemination

and environmental biosafety assessment. However

determining the recipient hosts and distribution patterns of mobile genetic elements in complex environmental microbial communities remains a major technical challenge. Conventional approaches

including cultivation-based methods

metagenomic sequencing

and spatial association technologies

provide valuable information on genetic element dissemination or community genetic composition

but are often limited by host culturability

insufficient linkage between genetic elements and their hosts

and challenges in interpreting association signals. These limitations hinder comprehensive analysis of mobile genetic element host ranges

particularly in complex communities containing abundant uncultured microorganisms. Recently

RNA-addressable modification (RAM)

an engineered ribozyme-based molecular recording technology

has provided a new strategy for identifying the carriage states and host association patterns of HGT-related mobile genetic elements. RAM utilizes engineered group I intron ribozymes to mediate RNA information recording

linking mobile genetic element-encoded RNA barcodes with host 16S rRNA information and converting otherwise difficult-to-observe genetic element-host associations into detectable molecular records. Recent studies have applied RAM to plasmid conjugation and phage transduction systems

demonstrating its potential for revealing distinct host distribution patterns of different mobile genetic elements in complex microbial communities. This commentary reviews the molecular recording mechanism of RAM

its applications in HGT-related microbial community studies

and its current limitations

while further discussing its complementary relationship with existing approaches for analyzing genetic element–host associations. The major significance of RAM does not lie in replacing conventional HGT analysis strategies

but rather in changing how genetic element–host relationships are characterized by converting associations previously inferred from sequence data

spatial correlations

or cultivation-based validation into recordable molecular evidence. Importantly

RAM records genetic element–host association states at specific sampling time points rather than reconstructing complete HGT transmission histories. Future advances in engineered ribozyme optimization

integration with cumulative information storage systems

and expansion into ecologically relevant applications may further establish RAM as a molecular recording platform for investigating mobile genetic element distribution patterns and host association characteristics in microbial ecosystems.

关键词

Keywords

references

OCHMAN H , LAWRENCE J G , GROISMAN E A . Lateral gene transfer and the nature of bacterial innovation [J ] . Nature , 2000 , 405 ( 6784 ): 299 - 304 .

SOUCY S M , HUANG J , GOGARTEN J P . Horizontal gene transfer: building the web of life [J ] . Nature Reviews Genetics , 2015 , 16 ( 8 ): 472 - 482 .

BRITO I L . Examining horizontal gene transfer in microbial communities [J ] . Nature Reviews Microbiology , 2021 , 19 ( 7 ): 442 - 453 .

SLIZOVSKIY I B , OLIVA M , SETTLE J K , et al . Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes [J ] . Microbiome , 2022 , 10 ( 1 ): 185 .

RUBIN B E , DIAMOND S , CRESS B F , et al . Species- and site-specific genome editing in complex bacterial communities [J ] . Nature Microbiology , 2022 , 7 ( 1 ): 34 - 47 .

YAFFE E , RELMAN D A . Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation [J ] . Nature Microbiology , 2020 , 5 ( 2 ): 343 - 353 .

SPENCER S J , TAMMINEN M V , PREHEIM S P , et al . Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers [J ] . The ISME Journal , 2016 , 10 ( 2 ): 427 - 436 .

KRUGER K , GRABOWSKI P J , ZAUG A J , et al . Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena [J ] . Cell , 1982 , 31 ( 1 ): 147 - 157 .

GAMBILL L , STAUBUS A , MO K W , et al . A split ribozyme that links detection of a native RNA to orthogonal protein outputs [J ] . Nature Communications , 2023 , 14 : 543 .

LIM M Y T , TAN C , SUBHRAMANYAM C S , et al . A programmable ribozyme for RNA signal transduction [J ] . Nature Communications , 2026 , 17 : 1428 .

DOTSON P P II , JOHNSON A K , TESTA S M . Tetrahymena thermophila and Candida albicans group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction [J ] . Nucleic Acids Research , 2008 , 36 ( 16 ): 5281 - 5289 .

KALVAPALLE P B , STAUBUS A , DYSART M J , et al . Information storage across a microbial community using universal RNA barcoding [J ] . Nature Biotechnology , 2026 , 44 ( 2 ): 269 - 276 .

LATURNER Z W , DYSART M J , SCHWARTZ S K , et al . Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding [J ] . Nature Communications , 2026 , 17 ( 1 ): 4308 .

LIU Z X , ZHANG S Y , ZHU H Z , et al . Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage [J ] . Science , 2024 , 383 ( 6682 ): eadh4859 .

RILEY A T , ROBSON J M , ULANOVA A , et al . Generative and predictive neural networks for the design of functional RNA molecules [J ] . Nature Communications , 2025 , 16 : 4155 .

ZHANG M , YANCEY C , ZHANG C , et al . A DNA circuit that records molecular events [J ] . Science Advances , 2024 , 10 ( 14 ): eadn3329 .

LARSSON D G J , FLACH C F . Antibiotic resistance in the environment [J ] . Nature Reviews Microbiology , 2022 , 20 ( 5 ): 257 - 269 .

CHEMLA Y , LEVIN I , FAN Y , et al . Hyperspectral reporters for long-distance and wide-area detection of gene expression in living bacteria [J ] . Nature Biotechnology , 2026 , 44 ( 2 ): 258 - 268 .

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