Biology subjects

Mackereth, C. D.

Publications and source records attributed to Mackereth, C. D..

10 recordsLinked to original sources

bioRxiv2025

Unconventional DNA architecture in a dopamine-bound aptamer complex

Aptamers are oligonucleotides that have been selected to bind a particular target. Despite the growing popularity of functional DNA aptamers, there remains limited knowledge of their binding mechanisms as few have been characterized at the atomic level. Here we use NMR spectroscopy to obtain structural details of RKEC1, a shortened version of a DNA aptamer previously reported to bind dopamine. We find that RKEC1 forms a compact structure upon ligand binding that lacks any Watson-Crick duplex regions or G-quadruplex core, in stark contrast to nearly all predicted and observed DNA aptamer folds. The atomic details explain dopamine specificity amongst structurally similar compounds, and the determined DNA fold was used to guide biosensor design. The aptamer structure further suggests that DNA folding can access an extensive conformational landscape reminiscent of RNA, thus expanding the diversity traditionally captured by predictive algorithms.

biochemistry↗

bioRxiv2025

Regulation of cell proliferation by a novel feedback system on Cdk function

The proliferation of eukaryotic cells is regulated by a complex network of regulatory systems that promotes efficient cell cycle progression and ensures proper responses to the environment. Despite this complexity, the core inputs that are necessary and sufficient for robust alternation of DNA replication and mitosis are surprisingly simpler than anticipated. Indeed, fission yeast cells operating with an engineered minimal cell cycle network that lacks the highly conserved Wee1+Cdc25 feedback loops on Cdk1 function are viable, although slow growing. This provides a unique entry for evaluating how such simplified cells can evolve and improve their proliferation potential while exploring unknown mechanisms modulating cell cycle progression. Taking advantage of this model, we applied laboratory evolution assays to minimal fission yeast backgrounds and selected for the emergence of faster growing populations. We found that loss of the small disordered protein Spo12 brings about enhanced population growth in cells lacking the Wee1+Cdc25 mitotic switch. Importantly, we demonstrate that Spo12 defines a new and conserved family of inhibitors of the Cdk-counteracting phosphatase PP2A that are directly regulated by Cdk-dependent phosphorylation. Our results also reveal a trade-off associated with Spo12-dependent regulation, which may have implications for our understanding of the principles underlying the evolution of cell cycle control. Finally, our study highlights how combining simplified circuits with experimental evolution allows for uncovering regulatory elements that may be obscured by network complexity.

cell biology↗

bioRxiv2025

Paralog-specific intrabodies for PSD-93 and SAP102 expand the molecular toolkit to resolve excitatory synapse organization

A scarcity of live, paralog-specific tools has limited analysis of PSD-MAGUKs at excitatory synapses. To address this gap, we engineered small, 10FN3-derived binders that selectively recognize PSD-93 and SAP102 -alongside an enhanced PSD-95 reagent- and converted them into regulated, gene-encoded intrabodies for endogenous imaging. Through sequence-guided selection and targeted optimization, we obtained high-specificity reagents that label their native targets in neurons with minimal perturbation and support multiplexed live-cell and advanced imaging modalities. This toolkit enables differential visualization of MAGUK paralogs at native levels and provides a practical route to dissect their distinct contributions to synapse organization and plasticity.

bioengineering↗

bioRxiv2025

Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers

Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular. Here, we report quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs, however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, e.g., the nucleic-acid backbone bends or a base forms a non-standard hydrogen bond. These bends and non-canonical interactions are integral to form functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life-cycle, posing a future challenge for the community.

biophysics↗

bioRxiv2025

Helical foldamers as selective G-quadruplex ligands

We investigated the G-quadruplex binding selectivity of short aromatic oligoamide helical foldamers comprising quinoline (Q) and pyridine (P) units. We found that the foldamers prefer parallel G-quadruplex structures, especially when the external G-quartets are sterically accessible. A crystal structure of the tetramer QQPQ with the parallel G-quadruplex formed by dTGGGTTGGGTTGGGTTGGGT shows two quinoline subunits interacting with an external G-quartet through {pi}-stacking, and solution NMR confirms that the foldamer targets the 3 and 5 ends of this G-quadruplex. Foldamers can also selectively target sequence variants of the telomeric sequences containing adenine-to-thymine mutation in the loops. The conformational selectivity of foldamers originates from the bulkiness of oligomers with four or more subunits, which imposes steric restrictions on G-quadruplex binding. The flexibility provided by the pyridine subunits was also key to improve affinity. Mixed quinoline-pyridine foldamers are thus a promising class of selective G-quadruplex ligands, and their unique modular scaffold offers new avenues to further improve their affinity and selectivity.

biophysics↗

bioRxiv2024

Disordered regions of human eIF4B orchestrate a dynamic self-association landscape

Eukaryotic translation initiation factor eIF4B is required for efficient cap-dependent translation, it is overexpressed in cancer cells, and may influence stress granule formation. Due to the high degree of intrinsic disorder, eIF4B is rarely observed in cryo-EM structures of translation complexes and only ever by its single structured RNA recognition motif domain, leaving the molecular details of its large intrinsically disordered region (IDR) unknown. By integrating experiments and simulations we demonstrate that eIF4B IDR orchestrates and fine-tunes an intricate transition from monomers to a condensed phase, in which large-size dynamic oligomers form before mesoscopic phase separation. Single-molecule spectroscopy combined with molecular simulations enabled us to characterize the conformational ensembles and underlying intra- and intermolecular dynamics across the oligomerization transition. The observed sensitivity to ionic strength and molecular crowding in the self-association landscape suggests potential regulation of eIF4B nanoscopic and mesoscopic behaviors such as driven by protein modifications, binding partners or changes to the cellular environment.

biophysics↗

bioRxiv2023

Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin

Eukaryotic pre-mRNA is processed by a large multiprotein complex to accurately cleave the 3 end, and to catalyze the addition of the poly(A) tail. Within this cleavage and polyadenylation specificity factor (CPSF) machinery, the CPSF73 endonuclease subunit directly contacts both CPSF100 and the scaffold protein Symplekin to form a subcomplex known as the core cleavage complex (CCC) or mammalian cleavage factor (mCF). Here we have taken advantage of a stable CPSF73-CPSF100 minimal heterodimer from E. cuniculi to determine the solution structure formed by the first and second C-terminal domain (CTD1 and CTD2) of both proteins. We find a large number of contacts between both proteins in the complex, and notably in the region between CTD1 and CTD2. A similarity is also observed between CTD2 and the TATA-box binding protein (TBP) domains. Separately, we have determined the structure of the terminal CTD3 domain of CPSF73, which also belongs to the TBP domain family and is connected by a flexible linker to the rest of CPSF73. Biochemical assays demonstrate a key role for the CTD3 of CPSF73 in binding Symplekin, and structural models of the trimeric complex from other species allow for comparative analysis and support an overall conserved architecture.

biochemistry↗

bioRxiv2022

Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex

To eliminate specific or aberrant transcripts, eukaryotic cells use nuclear RNA-targeting complexes that deliver them to the exosome for degradation. S. pombe MTREC complex, and its human counterpart PAXT, are key players in this mechanism. Red1 and hZFC3H1 function as scaffolds of these respective complexes. Here, we present an NMR structure of a helix-turn-helix domain of Red1 in complex with the N-terminus of Iss10 and show this interaction is required for proper cellular growth and meiotic mRNA degradation. We also report a crystal structure of a Red1-Ars2 complex that explains the mutually exclusive interactions of hARS2 with various "ED/EGEI/L" motif-possessing RNA regulators such as hZFC3H1, hFLASH or hNCBP3. Finally, we show that both Red1 and hZFC3H1 homo-dimerize via their coiled-coil regions indicating that MTREC and PAXT likely function as dimers. Our results, combining structures of three Red1 binding interfaces with in vivo studies, provide mechanistic insights into conserved features of MTREC/PAXT architecture.

biochemistry↗

bioRxiv2021

Engineering paralog-specific PSD-95 synthetic binders as potent and minimally invasive imaging probes

Despite the constant advances in fluorescence imaging techniques, monitoring endogenous proteins still constitutes a major challenge in particular when considering dynamics studies or super-resolution imaging. We have recently evolved specific protein-based binders for PSD-95, the main postsynaptic scaffold proteins at excitatory synapses. Since the synthetic binders recognize epitopes not directly involved in the target protein activity, we consider them here as tools to develop endogenous PSD-95 imaging probes. After confirming their lack of impact on PSD-95 function, we validated their use as intrabody fluorescent probes. We further engineered the probes and demonstrated their usefulness in different super-resolution imaging modalities (STED, PALM and DNA-PAINT) in both live and fixed neurons. Finally, we exploited the binders to enrich at the synapse genetically encoded calcium reporters. Overall, we demonstrate that these evolved binders constitute a robust and efficient platform to selectively target and monitor endogenous PSD-95 using various fluorescence imaging techniques.

neuroscience↗

bioRxiv2019

Structural basis of UCUU RNA motif recognition by splicing factor RBM20

The vertebrate splicing factor RBM20 (RNA Binding Motif protein 20) regulates protein isoforms important for heart development and function, with mutations in the gene linked to cardiomyopathy. Previous studies have identified the four base RNA motif UCUU as a common element in pre-mRNA targeted by RBM20. Here, we have determined the structure of the RNA Recognition Motif (RRM) domain from mouse RBM20 bound to RNA containing a UCUU sequence. The atomic details show that the RRM domain spans a larger region than initially proposed in order to interact with the complete UCUU motif, with a well-folded C-terminal helix encoded by exon 8 critical for high affinity binding. This helix only forms upon binding RNA with the final uracil, and removing the helix reduces affinity as well as specificity. We therefore find that RBM20 uses a coupled folding-binding mechanism by the C-terminal helix to specifically recognize the UCUU RNA motif.

molecular biology↗