Biology subjects

Pape, T.

Publications and source records attributed to Pape, T..

8 recordsLinked to original sources

bioRxiv2026

A DNA-scaffolded Retron Ring Mediates Antiphage Immunity

Retrons are a diverse family of bacterial defence systems that couple reverse transcriptase (RT) activity to antiphage immunity by producing multicopy single-stranded DNA (msDNA). Yet, the molecular mechanisms by which most systems detect infection and execute immunity remain unknown. Here, we define the structure, immune sensing and effector mechanisms of retron type IX, composed of an RT, a non-coding RNA, a tandem KH-HTH subunit and a HEPN RNase effector. Retron IX confers robust protection against diverse bacteriophages. Cryo-EM and biochemical analyses reveal a supramolecular ring assembly composed of 8-10 repeating modules, spanning up to 230 [A] in diameter. Within this assembly, the msDNA scaffolds the outer rim inhibiting the HEPN ribonuclease in a catalytically poised state, with the active site occluded within the inner layer. We identify a phage-encoded PD-(D/E)XK nuclease as the immune trigger that cleaves the exposed msDNA stem-loop, leading to ring disassembly and HEPN effector release. Upon activation, the HEPN ribonucleases cleave tRNAs indiscriminately, inducing dormancy and blocking phage propagation. Our findings unveil how ring-shaped higher-order assembly controls enzymatic activities while allowing signal-specific activation and establish the ncRNA as an evolvable scaffold underlying the remarkable structural and defensive diversity of bacterial retron immune complexes.

microbiology↗

bioRxiv2026

Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism

Successful viral infection requires efficient adsorption to the target cell, followed by membrane penetration for genome translocation into the host cytoplasm. Bacteriophage T4 initiates infection by binding to Escherichia coli receptors, triggering sequential conformational changes that culminate in genome delivery through viral channels spanning the host cell envelope. Here, we resolved structures of bacteriophage T4 at discrete stages. This revealed how long tail fiber extension affects the baseplate to initiate tail contraction, and the channel formation by the tape measure protein for genome translocation. We further demonstrate that the virus-encoded superinfection exclusion protein Imm binds to the tape measure protein to prevent secondary infections. Our findings offer insights into the coordinated process of genome delivery and phage-encoded superinfection exclusion proteins that prevent genome translocation.

microbiology↗

bioRxiv2025

Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states.

Contractile injection systems (CISs) are phage-tail-like nanosyringes that mediate bacterial interactions by puncturing target cell membranes. Within these systems, Photorhabdus Virulence Cassettes (PVCs) can translocate toxins across eukaryotic target cell membranes. The structure of a PVC has been described at atomic level and engineered to deliver diverse protein cargoes into non-natively-targeted organisms. Despite the structural insights into several CISs, information on PVCs from other species and details on the contraction mechanism remain limited. Here, we present the single-particle cryo-electron microscopy structure of PlPVC1, a PVC from the nematode symbiont and insect pathogen Photorhabdus luminescens DJC, in both extended and contracted states. Our structure displays distinct structural features that differ from other CISs, such as a cage surrounding the central spike, a larger sheath adaptor, and a plug exposed to the tube lumen. Moreover, we present the structures of the PlPVC1 fiber as well as the baseplate of the contracted particle, yielding insight into the contraction mechanism. This study provides structural details of the contracted state of the PlPVC1 particle and supports the model in which contraction is triggered. Furthermore, it facilitates the comparison of PlPVC1 with other contractile systems and expands the scope of engineering opportunities for future biomedical and biotechnological applications.

molecular biology↗

bioRxiv2024

Harmonising digitised herbarium data to enhance biodiversity knowledge: creating an updated checklist for the flora of Greenland.

International efforts to digitise herbarium specimens provide the building blocks for a global digital herbarium. However, taxonomic changes and errors can result in inconsistencies when amalgamating specimen metadata, that compromise the assignment of occurrence records to correct taxa, and the subsequent interpretation of patterns in biodiversity. We present a novel workflow to mass-curate digital specimens. By employing existing digital taxonomic backbones, we aggregate specimen names by their accepted name and flag remaining cases for manual review. We then validate names using site-specific floras, balancing automation with taxonomic expert-based curation. Applying our workflow to the vascular plants of Greenland, we harmonised 175,266 digitised herbarium specimens and observations from 92 data providers from the Global Biodiversity Information Facility (GBIF). The harmonised metacollection for the Greenland flora contains 780 plant species. Our workflow increases the number of species known from Greenland compared to other currently available species checklists and increases the mean number of occurrences per species by 42.6. Our workflow illustrates the integration required in order to create a global, universally accessible digital herbarium, and shows how previous obstacles to database curation can be overcome through a combination of automation and expert curation. From the specific perspective of the Greenland flora, our approach arrives at a new checklist of taxa, a new curated metacollection of occurrence data, and revised estimates of plant richness. The list of taxa and their prevalence allow a new basis for biodiversity assessment and conservation planning. Societal Impact StatementDigitising plant collections has allowed for data to be aggregated across multiple collections, forming a single harmonised resource of unprecedented scale. This resource is only accurate once the database names are assigned to one accepted name per species. We established a semi-automated workflow for processing plant name data, leveraging taxonomic backbones and employing taxonomic expertise at key stages. Applying our workflow to the flora of Greenland, we developed a curated checklist of 780 species, capturing greater species richness than previously published, while also curating 175,266 plant records. Our findings redefine our knowledge of Greenlandic plant diversity, while harmonising a vast digital collection for further research.

ecology↗

bioRxiv2023

N-terminal toxin signal peptides efficiently load therapeutics into a natural nano-injection system

Targeted delivery of therapeutics to specific cells is a major bottleneck towards personalized medicine. The extracellular injection system (eCIS) of Serratia entomophila, the antifeeding prophage (Afp), promises potential for drug delivery purposes. However, the precise mechanism of action, toxin location, and Afp loading remain unclear. Here, we reveal a minimal N-terminal signal peptide (NtSP) of the toxin Afp18, that plays a key role in toxin packing. By engineering fusion proteins, we demonstrate that Afp18s NtSP can shuttle effectors for Afp loading. We packed non-eCIS effectors, including CRISPR-Cas protein Cas{Phi}-2 from Biggiephage, and a human antimicrobial peptide, LL37, into Afp. Additionally, NtSPs from eCIS effectors of other species facilitate loading of Cas{Phi}-2 into Afp. We observed cargo being packed inside the Afp tail tube through cryo-EM single particle analysis. The presented results enhance our understanding of eCIS toxin packing and contribute to their development as targeted delivery systems. TeaserA novel use of the Afp nano injection systems N-terminal signal peptide in targeted therapeutics delivery

molecular biology↗

bioRxiv2022

Structural and Mechanistic Basis of Substrate Transport by the Multidrug Transporter MRP4

Multidrug resistance-associated protein 4 (MRP4) is an ATP-binding cassette (ABC) transporter expressed at multiple tissue barriers where it actively extrudes a wide variety of drug compounds. Overexpression of MRP4 provides resistance to clinically used antineoplastic and antiviral agents, making it a highly attractive therapeutic target for countering multidrug resistance. Here we report the cryo-EM structures of multiple physiologically relevant states of membrane-embedded human MRP4, including complexes between MRP4 and two widely used chemotherapeutic agents and a complex between MRP4 and its native substrate. The structures display clear similarities and distinct differences in the coordination of these chemically diverse substrates and, in combination with functional and mutational analysis, reveal molecular details of the transport mechanism. Our study provides key insights regarding the basis of the unusually broad substrate specificity of MRP4 and constitutes an important contribution towards a general understanding of the versatile ensemble of multidrug transporters.

molecular biology↗

bioRxiv2021

Structure of the mini-RNA-guided endonuclease CRISPR-Cas{Phi}3

CRISPR-Cas{Phi} is a novel family of miniaturized RNA-guided endonucleases from phages 1,2. These novel ribonucleoproteins (RNPs) provide a compact scaffold gathering all key activities of a genome editing tool2. Here, we provide the first structural insight into Cas{Phi} singular DNA targeting and cleavage mechanism by determining the cryoEM structure of Cas{Phi}3 with the triple strand R-loop generated after DNA cleavage. The structure reveals the unique machinery for target unwinding to form the crRNA-DNA hybrid and cleaving the target DNA. The protospacer adjacent motif (PAM) is recognised by the target strand (T-strand) and non-target strand (NT-strand) PAM interacting domains (TPID and NPID). Unwinding occurs after insertion of the conserved 1 helix disrupting the dsDNA, thus facilitating the crRNA-DNA hybrid formation. The NT-strand is funnelled towards the RuvC catalytic site, while a long helix of TPID separates the displaced NT-strand and the crRNA-DNA hybrid avoiding DNA re-annealing. The crRNA-DNA hybrid is directed to the stop (STP) domain that splits the hybrid guiding the T-strand towards the RuvC active site. The conserved RuvC insertion of the Cas{Phi} family is extended along the hybrid, interacting with the phosphate backbone of the crRNA. A cluster of hydrophobic residues anchors the RuvC insertion in a cavity of the STP domain. The assembly of the hybrid promotes the shortening of the RuvC insertion, thus pulling the STP towards the RuvC active site to activate catalysis. These findings illustrate why Cas{Phi} unleashes unspecific cleavage activity, degrading ssDNA molecules after activation. Site-directed mutagenesis in key residues support Cas{Phi}3 target DNA and non-specific ssDNA cutting mechanism. Our analysis provides new avenues to redesign the compact CRISPR-Cas{Phi} nucleases for genome editing.

biochemistry↗

bioRxiv2020

Structures of the Cmr-βComplex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas

Cmr-{beta} is a Type III-B CRISPR-Cas complex that upon target RNA recognition unleashes a multifaceted immune response against invading genetic elements, including ssDNA cleavage, cyclic oligoadenylate synthesis, and also a unique UA-specific ssRNA hydrolysis by the Cmr2 subunit. Here, we present the structure-function relationship of Cmr-{beta} unveiling how binding of the target RNA regulates the Cmr2 activities. CryoEM analysis revealed the unique subunit architecture of Cmr-{beta} and captured the complex in different conformational stages of the immune response, including the non-cognate and cognate target-RNA bound complexes. The binding of the target RNA induces a conformational change of Cmr2, which together with the complementation between the 5-handle in the crRNA and the 3-antitag of the target RNA, activate different configurations in a unique loop of the Cmr3 subunit, which acts as an allosteric sensor signaling the self vs. non-self recognition. These findings highlight the diverse defense strategies of Type III complexes.

biochemistry↗