A bacterial Argonaute with efficient DNA and RNA cleavage activity guided by small DNA and RNA

An Engineered PfAgo with Wide Catalytic Temperature Range and Substrate Spectrum

PfAgo, a thermophilic Argonaute nuclease from Pyrococcus furiosus, is widely used in various fields due to its high DNA-guided DNA cleavage activity. However, its high-temperature-dependent cleavage activity largely restricts its applications in moderate-temperature scenarios. In this study, PfAgo is engineered for cold adaptation based on its ternary complex structure and the attributes of cold-adapted enzymes, yielding a series of variants with better performance at moderate temperatures. Among those, mPfAgo (K617G, L618G) exhibits significantly promoted cleavage activity at 37 °C and a wider catalytic temperature range of 30-95 °C. Its high-temperature cleavage activity is also greatly improved, enabling its application in DNA detection with attomolar sensitivity in the presence of Mg2+. Additionally, mPfAgo shows versatile cleavage activities, including DNA cleavage guided by 5'OH-gDNA, 5'P-gDNA, or 5'COOH-gDNA, as well as RNA cleavage with 5'OH-gDNA, 5'P-gDNA, 5'P-gRNA, or 5'COOH-gDNA as guides. Further analysis through far-UV CD spectra and DSF indicates that mPfAgo has a more flexible structure than wild-type PfAgo. Furthermore, this established strategy is applied to engineer TtdAgo, likewise obtaining its variants with enhanced moderate-temperature activity and expanded substrate spectrum. In summary, this work provides a novel method for the rational design of thermophilic Agos, thereby greatly expanding their application scopes.

Argonaute-driven programmable multi-enzyme complex assembly on ribosomal RNA scaffolds

Scaffold-based multi-enzyme assembly strategies have significantly advanced biocatalysis by enhancing reaction efficiency through precise spatial organization of enzymes. While DNA- and protein-based scaffolds have been extensively studied, RNA scaffolds present unique advantages, including structural flexibility, dynamic regulation, and functional diversity. However, their application in vitro has been limited due to challenges related to stability and cost. Here, we developed a programmable RNA scaffold system that leverages catalytically inactive MbpAgo to spatially organize natural protein macromolecules into multi-enzyme complexes for in vitro cascade reactions. This strategy significantly enhances the catalytic efficiency of multi-enzyme systems in vitro. We utilized Förster resonance energy transfer experiments demonstrated tunable protein localization along the scaffold. By designing short guide DNAs (gDNAs) to direct MbpAgo-enzyme assembly onto yeast ribosomal RNA scaffolds, we achieved precise positioning of three enzymes in the ATP biosynthesis pathway, resulting in a 5.5-fold increase in catalytic yield after 3 h compared to scaffold-free multi-enzyme complexes. Additionally, the modular design of the Ago-gDNA-RNA scaffold system allows for dynamic reconfiguration of enzyme arrangements through simple modifications of gDNAs, enabling adaptability to diverse multi-enzyme reactions. This study underscores the potential of Argonaute-mediated RNA scaffolds as a versatile and efficient platform for in vitro multi-enzyme assembly.

Highly efficient loop cleavage for human papillomavirus detection with a novel thermophilic Argonaute from Thermus brockianus

Argonaute proteins (Agos), endowed with the capacity to cleave DNA or RNA under the guidance of small nucleic acid guides, have emerged as versatile biotechnological tools. This study endeavored to characterize a novel thermophilic Argonaute protein from Thermus brockianus (TbAgo), revealing its proficiency as a DNA-guided DNA endonuclease. Demonstrating high catalytic efficiency and precision at 65 °C, TbAgo possessed compatibility with loop-mediated isothermal amplification (LAMP) method, whose optimal temperature is also around 65 °C. Therefore, an innovative isothermal nucleic acid detection platform named AMEND (Argonaute-mediated loop cleavage for nucleic acid detection) was developed by integrating LAMP with TbAgo's targeted cleavage. This novel detection strategy was used to detect human papillomavirus (HPV) 16 and 18 DNA simultaneously with the limit of detection (LoD) of 1 aM within 30 min. Furthermore, a two-step microfluidic chip was designed to streamline the above HPV DNA detection workflow with high sensitivity of HPV 16 (1 aM) and 18 (10 aM) within 30 min. The present work not only characterized a novel Argonaute protein with the highest cleavage efficiency among the literature, but also paved the way to coordinate and streamline the two sequential reactions (isothermal DNA amplification and Ago mediated cleavage) at the same optimal temperature for high-efficiency DNA detection.

A mesophilic Argonaute from Clostridium formicaceticum with efficient DNA cleavage activity guided by small DNA

We characterized a new Argonaute protein (pAgo), CfAgo, from the mesophilic bacterium Clostridium formicaceticum. CfAgo possesses DNA-guided DNA endonuclease activity and cleaves DNA targets at the canonical site. It is active from 28°C to 75°C and prefers DNA guides with a 5'-phosphate group and thymidine as the first nucleotide. Cleavage activity is reduced by single-nucleotide mismatches in the seed, central, and 3'-supplementary regions of guides, with stronger mismatch discrimination observed for 5'hydroxylated (5'OH) guides compared to 5'phosphorylated (5'P) guides. Moreover, structural analysis suggests that the MID domain of CfAgo is crucial for recognizing the 5' guide and it influences the binding specificity. CfAgo catalyzes programmable cleavage of double-stranded DNA in AT-rich regions in the presence of Mn2+ and Mg2+ ions at appropriate salt concentrations. These properties could make CfAgo a promising tool for DNA manipulation such as nucleic acid detection and cleavage.

Structural basis of ssDNA-guided NADase activation of prokaryotic SPARTA system

Short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins constitute a prokaryotic immune system, mediating RNA- or DNA-guided target single-stranded DNA (ssDNA) to activate NADase activity and induce cell death by degrading NAD+ in response to invading plasmids. Although the guide RNA-mediated targeting mechanism of SPARTA has been established, the functional role and mechanisms of guide DNA-mediated SPARTA remain poorly understood. Here, we report two crystal structures of Crenotalea thermophila SPARTA complexes with 5'-phosphorylated 21-nt guide DNA and complementary target ssDNA lengths of 15 or 20 nt. The structures demonstrate specific recognition of the 5'-OH or 3'-OH groups in target DNA by SPARTA, while not recognizing the 5'-P group in guide DNA. This suggests distinct recognition models for guide DNA and guide RNA, indicating different activation mechanisms. Furthermore, these two structures reveal disparate models for recognizing guide DNA and target DNA, providing insights into the length requirement for SPARTA activation.

Efficient genome-editing tools to engineer the recalcitrant non-model industrial microorganism Zymomonas mobilis

Current biotechnology relies on a few well-studied model organisms, such as Escherichia coli and Saccharomyces cerevisiae, for which abundant information and efficient toolkits are available for genetic manipulation, but which lack industrially favorable characteristics. Non-model industrial microorganisms usually do not have effective and/or efficient genome-engineering toolkits, which hampers the development of microbial cell factories to meet the fast-growing bioeconomy. In this study, using the non-model ethanologenic bacterium Zymomonas mobilis as an example, we developed a workflow to mine and temper the elements of restriction-modification (R-M), CRISPR/Cas, toxin-antitoxin (T-A) systems, and native plasmids, which are hidden within industrial microorganisms themselves, as efficient genome-editing toolkits, and established a genome-wide iterative and continuous editing (GW-ICE) system for continuous genome editing with high efficiency. This research not only provides tools and pipelines for engineering the non-model polyploid industrial microorganism Z. mobilis efficiently, but also sets a paradigm to overcome biotechnological limitations in other genetically recalcitrant non-model industrial microorganisms.

Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation

Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.

Mn2+-induced structural flexibility enhances the entire catalytic cycle and the cleavage of mismatches in prokaryotic argonaute proteins

Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid-based biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+ in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicate that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+ in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.

The nuclease-associated short prokaryotic Argonaute system nonspecifically degrades DNA upon activation by target recognition

Prokaryotic Argonautes (pAgos) play a vital role in host defense by utilizing short nucleic acid guides to recognize and target complementary nucleic acids. Despite being the majority of pAgos, short pAgos have only recently received attention. Short pAgos are often associated with proteins containing an APAZ domain and a nuclease domain including DUF4365, SMEK, or HNH domain. In contrast to long pAgos that specifically cleave the target DNA, our study demonstrates that the short pAgo from Thermocrispum municipal, along with its associated DUF4365-APAZ protein, forms a heterodimeric complex. Upon RNA-guided target DNA recognition, this complex is activated to nonspecifically cleave DNA. Additionally, we found that the TmuRE-Ago complex shows a preference for 5'-OH guide RNA, specifically requires a uridine nucleotide at the 5' end of the guide RNA, and is sensitive to single-nucleotide mismatches between the guide RNA and target DNA. Based on its catalytic properties, our study has established a novel nucleic acid detection method and demonstrated its feasibility. This study not only expands our understanding of the defense mechanism employed by short pAgo systems but also suggests their potential applications in nucleic acid detection.

Prokaryotic Argonautes for in vivo biotechnology and molecular diagnostics

Prokaryotic Argonautes (pAgos) are an emerging class of programmable endonucleases that are believed to be more flexible than existing CRISPR-Cas systems and have significant potential for biotechnology. Current applications of pAgos include a myriad of molecular diagnostics and in vitro DNA assembly tools. However, efforts have historically been centered on thermophilic pAgo variants. To enable in vivo biotechnological applications such as gene editing, focus has shifted to pAgos from mesophilic organisms. We discuss what is known of pAgos, how they are being developed for various applications, and strategies to overcome current challenges to in vivo applications in prokaryotes and eukaryotes.

Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection

Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Diverse prokaryotic Agos (pAgos) play potential functions in microbial defense. The functions and mechanisms of a group of full-length yet catalytically inactive pAgos, long-B pAgos, remain unclear. Here, we show that most long-B pAgos are functionally connected with distinct associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. The long-B pAgo-nuclease system (BPAN) is activated by guide RNA-directed target DNA recognition and performs collateral DNA degradation in vitro. In vivo, the system mediates genomic DNA degradation after sensing invading plasmid, which kills the infected cells and results in the depletion of the invader from the cell population. Together, the BPAN system provides immunoprotection via abortive infection. Our data also suggest that the defense strategy is employed by other long-B pAgos equipped with distinct associated proteins.

Programmable site-specific DNA double-strand breaks via PNA-assisted prokaryotic Argonautes

Programmable site-specific nucleases promise to unlock myriad applications in basic biology research, biotechnology and gene therapy. Gene-editing systems have revolutionized our ability to engineer genomes across diverse eukaryotic species. However, key challenges, including delivery, specificity and targeting organellar genomes, pose barriers to translational applications. Here, we use peptide nucleic acids (PNAs) to facilitate precise DNA strand invasion and unwinding, enabling prokaryotic Argonaute (pAgo) proteins to specifically bind displaced single-stranded DNA and introduce site-specific double-strand breaks (DSBs) independent of the target sequence. We named this technology PNA-assisted pAgo editing (PNP editing) and determined key parameters for designing PNP editors to efficiently generate programable site-specific DSBs. Our design allows the simultaneous use of multiple PNP editors to generate multiple site-specific DSBs, thereby informing design considerations for potential in vitro and in vivo applications, including genome editing.

Argonaute protein-based nucleic acid detection technology

It is vital to diagnose pathogens quickly and effectively in the research and treatment of disease. Argonaute (Ago) proteins are recently discovered nucleases with nucleic acid shearing activity that exhibit specific recognition properties beyond CRISPR-Cas nucleases, which are highly researched but restricted PAM sequence recognition. Therefore, research on Ago protein-mediated nucleic acid detection technology has attracted significant attention from researchers in recent years. Using Ago proteins in developing nucleic acid detection platforms can enable efficient, convenient, and rapid nucleic acid detection and pathogen diagnosis, which is of great importance for human life and health and technological development. In this article, we introduce the structure and function of Argonaute proteins and discuss the latest advances in their use in nucleic acid detection.

Structural insights into mechanisms of Argonaute protein-associated NADase activation in bacterial immunity

Nicotinamide adenine dinucleotide (NAD+) is a central metabolite in cellular processes. Depletion of NAD+ has been demonstrated to be a prevalent theme in both prokaryotic and eukaryotic immune responses. Short prokaryotic Argonaute proteins (Agos) are associated with NADase domain-containing proteins (TIR-APAZ or SIR2-APAZ) encoded in the same operon. They confer immunity against mobile genetic elements, such as bacteriophages and plasmids, by inducing NAD+ depletion upon recognition of target nucleic acids. However, the molecular mechanisms underlying the activation of such prokaryotic NADase/Ago immune systems remain unknown. Here, we report multiple cryo-EM structures of NADase/Ago complexes from two distinct systems (TIR-APAZ/Ago and SIR2-APAZ/Ago). Target DNA binding triggers tetramerization of the TIR-APAZ/Ago complex by a cooperative self-assembly mechanism, while the heterodimeric SIR2-APAZ/Ago complex does not assemble into higher-order oligomers upon target DNA binding. However, the NADase activities of these two systems are unleashed via a similar closed-to-open transition of the catalytic pocket, albeit by different mechanisms. Furthermore, a functionally conserved sensor loop is employed to inspect the guide RNA-target DNA base pairing and facilitate the conformational rearrangement of Ago proteins required for the activation of these two systems. Overall, our study reveals the mechanistic diversity and similarity of Ago protein-associated NADase systems in prokaryotic immune response.

Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo

Prokaryotic Argonaute proteins (pAgos) are homologs of eukaryotic Argonautes (eAgos) and are also thought to play a role in cell defense against invaders. However, pAgos are much more diverse than eAgos and little is known about their functional activities and target specificities in vivo. Here, we describe five pAgos from mesophilic bacteria that act as programmable DNA endonucleases and analyze their ability to target chromosomal and invader DNA. In vitro, the analyzed proteins use small guide DNAs for precise cleavage of single-stranded DNA at a wide range of temperatures. Upon their expression in Escherichia coli, all five pAgos are loaded with small DNAs preferentially produced from plasmids and chromosomal regions of replication termination. One of the tested pAgos, EmaAgo from Exiguobacterium marinum, can induce DNA interference between homologous sequences resulting in targeted processing of multicopy plasmid and genomic elements. EmaAgo also protects bacteria from bacteriophage infection, by loading phage-derived guide DNAs and decreasing phage DNA content and phage titers. Thus, the ability of pAgos to target multicopy elements may be crucial for their protective function. The wide spectrum of pAgo activities suggests that they may have diverse functions in vivo and paves the way for their use in biotechnology.