Biology subjects

Nichols, P. J.

Publications and source records attributed to Nichols, P. J..

5 recordsLinked to original sources

bioRxiv2026

C. elegans Dicer stacks with the RIG-I-like receptor DRH-1 to cleave dsRNA

In prior studies we showed that the nematode ancestor of Dicer's helicase domain had minimal ATP hydrolysis, translocation and dsRNA binding activity, and in extant C. elegans the RIG-I like receptor (RLR) DRH-1, and the dsRNA binding protein RDE-4, were co-opted to provide these activities. Here we report cleavage-competent cryo-EM structures of the antiviral complex (AVC; DCR-1{middle dot}DRH-1{middle dot}RDE-4), in the absence (3.2[A]) and presence (3.0[A] of ATP. A key feature of both structures is stacking of DCR-1's helicase with the helicases of two DRH-1 molecules, reminiscent of oligomerization of mammalian RLRs. dsRNA threads through all three helicases with a widened major groove at helicase-helicase interfaces and where the conserved Hel2 loop inserts into the major groove. The presence of nucleotide redistributed helicase-helicase and helicase-RNA contacts in the AVC, as for MDA5, albeit specific interactions and remodeling differed. MDA5 and RIG-I RLRs contain an unstructured linker between their CARDs and helicase domain, but the analogous linker in DRH-1 has a short-structured region positioned to interact with DCR-1. These findings provide a structural framework for understanding how DCR-1, DRH-1, and RDE-4 cooperate to cleave viral dsRNA and elucidate unique features required for antiviral defense in different animals.

immunology↗

bioRxiv2026

ZBP1's Inability to Convert Unmodified RNAs to the Z-form Underlies a Balanced Mechanism of RNA Recognition with ADAR1

Z-DNA Binding Protein 1 (ZBP1) is a critical pattern recognition receptor within the innate immune response to viral infection. ZBP1 senses foreign nucleic acids in the unusual, left-handed Z-conformation via binding through its N-terminal Z1 and Z2 domains and activates downstream pro-pyroptotic, -apoptotic, and -necroptotic pathways to initiate cell death and allow for viral clearance. Both dsDNA and dsRNA can adopt the Z-conformation, however, the conformational change is energetically expensive, especially for dsRNA, and typically requires chemical modifications or protein binding to induce a right-to-left-handed conversion and stabilization. ZBP1 has been previously shown to bind and convert B-DNA to the Z-conformation and was assumed to be able to convert A-RNA as well, despite the lack of experimental validation. Here, we use a variety of Nuclear Magnetic Resonance (NMR) and other biophysical and biochemical experiments to characterize the Z-DNA and Z-RNA binding properties of ZBP1s Z1 and Z2 domains. While ZBP1s Z domains are able to convert and stabilize unmodified dsDNA in the Z-conformation, both domains are incapable of flipping unmodified A-conformation dsRNA. We show that ZBP1s Z domains require dsRNAs with Z-promoting chemical modification in order for them to bind and stabilize the Z-conformation. These results contrast with the Z domain from Adenosine Deaminase Acting on RNA 1 (ADAR1), which can bind and flip both dsDNA and dsRNA into the Z-conformation, potentially indicating finely tuned competition between ADAR1 and ZBP1 for pro-survival and pro-death outcomes, respectively. This work highlights the functional variability of Z domains and narrows down the potential physiological substrates of ZBP1 in infection and disease. Graphical O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/719927v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@11a03caorg.highwire.dtl.DTLVardef@eec771org.highwire.dtl.DTLVardef@67d152org.highwire.dtl.DTLVardef@1df808d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Z-Form Stabilization By The Zα Domain Of Adar1p150 Has Subtle Effects On A-To-I Editing

The role of Adenosine Deaminase Acting on RNA 1 (ADAR1)s Z-conformation stabilizing Z domain in A-to-I editing is unclear. Previous studies on Z mutations faced limitations, including variable ADAR1p150 expression, differential editing analysis challenges, and unaccounted changes in ADAR1p150 localization. To address these issues, we developed a Cre-lox system in ADAR1p150 KO cells to generate stable cell lines expressing Z mutant ADAR1p150 constructs. Using total RNA sequencing analyzing editing clusters as a proxy for dsRNAs, we found that Z mutations slightly decreased overall A-to-I editing, consistent with recent findings. These decreases correlated with mislocalization of ADAR1p150 rather than reduced editing specificity, and practically no statistically significant differentially edited sites were identified between wild-type and Z mutant ADAR1p150 constructs. These results suggest that Zs impact on editing is minor and that phenotypes in Z mutant mouse models and human patients may arise from editing-independent inhibition of Z-DNA-Binding Protein 1 (ZBP1), rather than changes in RNA editing.

cell biology↗

bioRxiv2020

A new subclass of exoribonuclease resistant RNA found in multiple Flaviviridae genera

Viruses have developed innovative strategies to exploit the cellular machinery and overcome the host antiviral defenses, often using specifically structured RNA elements. Examples are found in flaviviruses; during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5 to 3 exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease resistant RNA structure (xrRNA) located in the viral genomes 3untranslated region (UTR). Although known to exist in several Flaviviridae genera the full distribution and diversity of xRNAs in this virus family was unknown. Using the recent high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNA in the Pegivirus, Pestivirus, and Hepacivirus genera. We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Our findings thus require adjustments of previous xrRNA classification schemes and expand on the previously known distribution of the xrRNA in Flaviviridae, indicating their widespread distribution and illustrating their importance. IMPORTANCEThe Flaviviridae comprise one of the largest families of positive sense single stranded (+ssRNA) and it is divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika Virus, Dengue Virus, and Powassan Virus. In these, a part of the viruss RNA twists up into a very special three-dimensional shape called an xrRNA that blocks the ability of the cell to "chew up" the viral RNA. Hence, part of the virus RNA remains intact, and this protected part is important for viral infection. This was known to occur in Flaviviruses but whether it existed in the other members of the family was not known. In this study, we not only identified a new subclass of xrRNA found in Flavivirus but also in the remaining three genera. The fact that this process of viral RNA maturation exists throughout the entire Flaviviridae family makes it clear that this is an important but underappreciated part of the infection strategy of these diverse human pathogens.

microbiology↗

bioRxiv2019

Molecular Dynamics Simulations,Exact NOE Measurements, and Machine Learning Reveal a Low-populated State of the UUCG RNA Tetraloop

We provide an atomic-level description of the structure and dynamics of the UUCG RNA stem-loop by combining molecular dynamics simulations with experimental data. The integration of simulations with exact nuclear Overhauser enhancements data allowed us to characterize two distinct states of this molecule. The most stable conformation corresponds to the consensus three-dimensional structure. The second state is characterized by the absence of the peculiar non-Watson-Crick interactions in the loop region. By using machine learning techniques we identify a set of experimental measurements that are most sensitive to the presence of non-native states. We find that although our MD ensemble, as well as the consensus UUCG tetraloop structures, are in good agreement with experiments, there are remaining discrepancies. Together, our results show that i) the structural interpretation of experimental data for dynamic RNAs is highly complex, even for a simple model system such as the UUCG tetraloop ii) the MD simulation overstabilize a non-native loop conformation, and iii) eNOE data support its presence with a population of {approx}10%.

biophysics↗