Jana Škerlová

Discovery of functional nucleic acids from randomized libraries typically relies on multiple, time-consuming iterative rounds of in vitro selection with low success rate. Here, we present a single-round selection strategy for rapid screening of multiple over-represented nucleobase-modified DNA libraries and various selection conditions, capable of identifying high-affinity modified aptamers. Double partition followed by amplification of eluted sequences, NGS analysis and clustering provides fast identification of aptamer candidates. Screening of modified DNA libraries containing modified adenine and uracil nucleotides bearing hydrophobic aromatic phenyl and indole moieties results in development of an aptamer binding human insulin receptor with sub-nanomolar affinity and exquisite specificity. Cryo-EM structure reveals the importance of each aromatic modification, either in stabilizing the secondary structure or facilitating interactions with the protein surface. This approach addresses the main drawbacks of aptamer selection and has potential for high-throughput screening and accelerating the development of next-generation aptamers for diagnostics or therapeutics.

RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside polyphosphates by RNA polymerase as noncanonical initiating nucleotides. However, how these compounds bind into the active site of RNA polymerase during transcription initiation is unknown. Here, we explored transcription initiation in vitro, using a series of DNA templates in combination with dinucleoside polyphosphates and model RNA polymerase from Thermus thermophilus . We observed that the transcription start site can vary on the basis of the compatibility of the specific template and dinucleoside polyphosphate. Cryo-electron microscopy structures of transcription initiation complexes with dinucleoside polyphosphates revealed that both nucleobase moieties can pair with the DNA template. The first encoded nucleotide pairs in a canonical Watson–Crick manner, whereas the second nucleobase pairs noncanonically in a reverse Watson–Crick manner. Our work provides a structural explanation of how dinucleoside polyphosphates initiate RNA transcription.

Discovery of functional nucleic acid ligands and catalytic motifs from a vast sequence space of randomized libraries is mostly based on time-consuming and demanding iterative rounds of in vitro selection. Here, we present a streamlined method for rapid identification of nucleobase-modified aptamers in a single selection round by combining chemically modified over-represented libraries, consecutive partition steps, and sequence abundance distribution analysis coupled with clustering. This approach generates distinct clusters of sequences, avoiding the need for massive screening of aptamer candidates. We demonstrated the proof-of-principle and effectiveness of the single-round selection approach resulting in a human insulin receptor aptamer, moreover, this method offers the expedient ability to screen multiple targets, various selection conditions, or differently modified libraries in a parallelized manner. The modified aptamer composed of two hydrophobic indole- and phenyl-linked nucleotides and two natural nucleotides exhibited picomolar binding affinity and exquisite specificity, capable of distinguishing subtle amino acid variations. Additionally, we determined the structure of the aptamer-receptor complex using cryo-electron microscopy, confirming the crucial role of hydrophobic aromatic modifications for the interactions of the aptamer with the target protein. These results highlight the synergistic effect of the components involved and demonstrate the capability of this methodology to generate highly potent and specific modified aptamers without tedious iterative selection rounds and extensive sequence space, thus accelerating aptamer discovery for therapeutic and diagnostic applications.

Human aldo-keto reductase 1C3 (AKR1C3) is a steroid modifying enzyme involved in cancer progression. Here, A-ring modified 17α-picolyl and 17(E)-picolinylidene androstane derivatives are shown to inhibit AKR1C3 activity in vitro. None of the androstane derivatives have off-target affinity for the androgen receptor, based on a fluorescence assay in yeast cells. The X-ray structure of AKR1C3 in complex with the strongest inhibitor, a 17α-picolyl androstane with a C3-oxime modification, was determined at 1.7 Å resolution. Based on this crystal structure and molecular docking, inhibition of AKR1C3 by the 17α-picolyl or 17(E)-picolinylidene derivatives depends on interactions between the C3 modification and the NADP⁺ cofactor, while the C17α-picolyl or C17-picolinylidene group anchors the inhibitor to AKR1C3. Because one AKR1C3 inhibitor identified here was also previously reported to inhibit CYP17, it may be possible for future researchers to design dual AKR1C3/CYP17 inhibitors based on a steroid scaffold for potential treatment of advanced prostate cancers.

Botulinum neurotoxins (BoNTs) are the most potent toxins known and are used to treat an increasing number of medical disorders. All BoNTs are naturally co-expressed with a protective partner protein (NTNH) with which they form a 300 kDa complex, to resist acidic and proteolytic attack from the digestive tract. We have previously identified a new botulinum neurotoxin serotype, BoNT/X, that has unique and therapeutically attractive properties. We present the cryo-EM structure of the BoNT/X-NTNH/X complex and the crystal structure of the isolated NTNH protein. Unexpectedly, the BoNT/X complex is stable and protease-resistant at both neutral and acidic pH and disassembles only in alkaline conditions. Using the stabilizing effect of NTNH, we isolated BoNT/X and showed that it has very low potency both in vitro and in vivo. Given the high catalytic activity and translocation efficacy of BoNT/X, low activity of the full toxin is likely due to the receptor-binding domain, which presents very weak ganglioside binding and exposed hydrophobic surfaces.

The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography and cryo-electron microscopy to investigate architecture and functional mechanism of two prototypical representatives of two sub-classes of the SorC family: DeoR and CggR from Bacillus subtilis. Despite possessing distinct DNA-binding domains, both proteins form similar tetrameric assemblies when bound to their respective DNA operators. Structural analysis elucidates the process by which the CggR-regulated gapA operon is derepressed through the action of two effectors: fructose-1,6-bisphosphate and newly confirmed dihydroxyacetone phosphate. Our findings provide the first comprehensive understanding of the DNA binding mechanism of the SorC-family proteins, shedding new light on their functional characteristics.

The botulinum neurotoxin‐like toxin from Weissella oryzae (BoNT/Wo) is one of the BoNT‐like toxins recently identified outside of the Clostridium genus. We show that, like the canonical BoNTs, BoNT/Wo forms a complex with its non‐toxic non‐hemagglutinin (NTNH) partner, which in traditional BoNT serotypes protects the toxin from proteases and the acidic environment of the hosts' guts. We here report the cryo‐EM structure of the 300 kDa BoNT/Wo‐NTNH/Wo complex together with pH stability studies of the complex. The structure reveals molecular details of the toxin's interactions with its protective partner. The overall structural arrangement is similar to other reported BoNT‐NTNH complexes, but NTNH/Wo uniquely contains two extra bacterial immunoglobulin‐like (Big) domains on the C‐terminus. Although the function of these Big domains is unknown, they are structurally most similar to bacterial proteins involved in adhesion to host cells. In addition, the BoNT/Wo protease domain contains an internal disulfide bond not seen in other BoNTs. Mass photometry analysis revealed that the BoNT/Wo‐NTNH/Wo complex is stable under acidic conditions and may dissociate at neutral to basic pH. These findings established that BoNT/Wo‐NTNH/Wo shares the general fold of canonical BoNT–NTNH complexes. The presence of unique structural features suggests that it may have an alternative mode of activation, translocation and recognition of host cells, raising interesting questions about the activity and the mechanism of action of BoNT/Wo as well as about its target environment, receptors and substrates.

Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription regulatory factors. Although various modification states of a particular histone residue often lead to differential outcomes, it is not entirely clear how they are discriminated. Moreover, the contribution of intrinsically disordered regions outside of the specialized reader domains to nucleosome binding remains unexplored. Here, we report the structures of a PWWP domain from transcriptional coactivator LEDGF in complex with the H3K36 di- and trimethylated nucleosome, indicating that both methylation marks are recognized by PWWP in a highly conserved manner. We identify a unique secondary interaction site for the PWWP domain at the interface between the acidic patch and nucleosomal DNA that might contribute to an H3K36-methylation independent role of LEDGF. We reveal DNA interacting motifs in the intrinsically disordered region of LEDGF that discriminate between the intra- or extranucleosomal DNA but remain dynamic in the context of dinucleosomes. The interplay between the LEDGF H3K36-methylation reader and protein binding module mediated by multivalent interactions of the intrinsically disordered linker with chromatin might help direct the elongation machinery to the vicinity of RNA polymerase II, thereby facilitating productive elongation.