Biology subjects

Krall, J. B.

Publications and source records attributed to Krall, J. B..

4 recordsLinked to original sources

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

Zα and Zβ domains of ADAR1 and ZBP1 bind to G-quadruplexes with low micromolar affinity

1While it is well established that the Z domains of ADAR1 and ZBP1 proteins bind Z-form-prone nucleic acids (Z-NAs), it has also been shown that the Z domain of ADAR1 binds DNA G-Quadruplexes (GQ). However, no binding partner of the structurally homologous Z{beta} domain of ADAR1 has been identified to date. Based on AlphaFold and molecular dynamics simulations, it has recently been suggested that the Z{beta} domain of ADAR1 targets its substrate by recognizing GQs. Here, we provide the first experimental evidence for Z{beta} domain binding to select G-quadruplex RNA and DNA in vitro, with structural specificity and low micromolar affinity. We also demonstrate that the Z domains of ZBP1 bind to both DNA and RNA GQs with similar affinity. These findings extend the range of potential functional roles for these proteins and open new hypotheses for testing in cells.

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↗

bioRxiv2022

Deepwater Horizon crude oil reduces aerobic capacity of birds

Crude oil spills can have catastrophic effects on marine and inland ecosystems, yet it is difficult to accurately quantify the extent of ecological damage caused by oil spills. For instance, avian population damage assessments conducted after large oil spills (e.g., Deepwater Horizon spill) often focus on the number of visibly oiled birds. However, birds without visible oiling can exhibit hematological damage from oil ingestion. If such hematological responses limit oxygen deliver to tissues and impair aerobic performance, then energy-mediated effects from oil ingestion may ultimately affect endpoints of demographic significance (e.g., survival and reproduction). We investigated whether oil ingestion affects aerobic performance in birds by orally dosing zebra finches (Taeniopygia guttata) with 2 or 6 mL/kg of weathered MC252 crude oil for 28 days. After 14 and 28 days of dosing, we measured hematological indices (oxidative damage, packed cell volume [PCV], hemoglobin, reticulocytes), maximum metabolic rate (MMR), resting metabolic rate (RMR), and short-distance flight performance. Finches exposed to oil exhibited lower hemoglobin and PCV, higher reticulocyte counts, and greater oxidative damage. Shifts in these hematological indices appeared to alter organismal energetics, resulting in reduced MMR, RMR, and aerobic scope. Short-distance burst-flight was not negatively impacted by oil ingestion. Collectively, these results suggest oil ingestion impairs metabolic performance, which may negatively impact a birds ability to perform sustained energetically expensive activities (e.g., migration). SignificanceThe 2010 Deepwater Horizon oil spill released an unprecedented volume of crude oil (MC252) into the northern Gulf of Mexico and contaminated 2100 km of shoreline habitat that serves as critical breeding grounds and migratory stop-over sites for birds. Here we describe the impact of oil ingestion on the aerobic capacity of zebra finches, a model songbird. Oil ingestion reduced maximum metabolic rate and aerobic scope, which may be caused in part by hematological damage. These data suggest oil ingestion limits the ability of birds to perform essential energetically demanding activities (e.g., migration, nest incubation), thus quantification of avian injury based on external oiling alone may underestimate the true impact of oil spills on avian populations.

pharmacology and toxicology↗