Scholarly Works, Biochemistry

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Biogenic Amine-Containing 1,4-Naphthoquinones Mediate Extracellular Electron Transfer in Lactiplantibacillus plantarum
Blackburn, Benjamin T.; Barton, Joseph; Hoernig, Micah; Brown, Anne M.; Mevers, Emily (American Chemical Society, 2025-09-19)
Lactiplantibacillus plantarum, a lactic acid gut bacterium, uses exogenous quinones to facilitate extracellular electron transfer (EET) via type II NADH dehydrogenase (Ndh2). To probe Ndh2 specificity, we designed and evaluated a library of biogenic amine-substituted 1,4-naphthoquinones in an Ndh2-dependent EET assay. Analysis of mediator Ndh2 binding interactions revealed that activity correlates with key binding interactions. Specifically, mediators containing aromatic substitutions elicit favorable Ndh2 interactions, promoting EET.
Chromosomal inversions and their potential impact on the evolution of arboviral vector Aedes aegypti
Liang, Jiangtao; Rose, Noah; Brusentsov, Ilya; Lukyanchikova, Varvara; Karagodin, Dmitriy; Feng, Yifan; Yurchenko, Andrey; Sharakhov, Igor V.; McBride, Carolyn; Sharakhova, Maria V. (Oxford University Press, 2024-06-29)
Chromosomal inversions play a crucial role in evolution and have been found to regulate epidemiologically significant traits in malaria mosquitoes. However, they have not been characterized in Aedes aegypti, the primary vector of arboviruses, due to the poor structure of its polytene chromosomes. The Hi-C proximity ligation approach was used to identify chromosomal inversions in 25 strains of A. aegypti obtained from its worldwide distribution and in one strain of Aedes mascarensis. The study identified 21 multimegabase polymorphic inversions ranging in size from 5 to 55 Mbp. Inversions were more abundant in African than in non-African strains, 15 versus 3 inversions, with the highest number observed in West Africa. All inversions were grouped into two geographic clusters of African or non-African origin, suggesting their association with A. aegypti subspecies. Inversions were unevenly distributed along chromosomal arms, with the highest number found in the 1q and 3p arms homologous to the inversion-rich 2R chromosomal arm in the malaria vector Anopheles gambiae. Direct comparison of inversions between A. aegypti and An. gambiae revealed significant overlap in their genomic locations. This finding may explain the parallel evolution of the two species under similar environmental conditions. Some of the inversions colocalized with chemoreceptor genes and quantitative trait loci associated with pathogen infection, suggesting their potential role in host preference and disease transmission. Our study revealed the large pool of structural variations in the A. aegypti genome and provides the foundation for future studies of their impact on the biology of this important arboviral vector.
Reductions in protein degradation in the retrosplenial cortex regulate contextual fear memory formation in a sex-independent manner
Turner, Meagan; Ball, Olivia; Ray, W. Keith; Helm, Richard F.; Jarome, Timothy J. (Elsevier, 2025-12-16)
The retrosplenial cortex (RSC), which serves as a hub to connect the hippocampus and amygdala with other cortical regions, has been shown to play a role in the formation of contextual fear memories. However, the molecular mechanisms by which the RSC forms memories and whether sex differences exist within these mechanisms remain largely unknown. Increases in ubiquitin–proteasome-mediated protein degradation have been shown to be sex-dependently involved in the formation of contextual fear memories in multiple brain regions, including the hippocampus and amygdala. To date, whether increases in protein degradation are needed in the RSC for memory formation in either sex has yet to be examined. Here, we found that proteasome function in the RSC decreases after contextual fear conditioning in both male and female rats. Consistent with this, increasing proteasome activity in the RSC via CRISPR-dCas9-mediated upregulation of Psmd14 impaired contextual fear memory in a mixed sex cohort. Interestingly, proteomic analysis of degradation-specific lysine-48 (K48) polyubiquitination in the RSC of fear-conditioned rats showed largely distinct protein degradation targets and impacted pathways across the sexes. This suggests that despite the shared need for reductions in protein degradation, males and females are using this mechanism in different ways to form the same memory. Together, these data demonstrate that reductions in protein degradation in the RSC are critical for contextual fear memory formation in both males and females and indicate that the molecular changes in the RSC during memory formation may be distinct from those of other more commonly studied brain regions.
Noninvasive Analysis of Peptidoglycan from Living Animals
Ocius, Karl L.; Kolli, Sree H.; Ahmad, Saadman S.; Dressler, Jules M.; Chordia, Mahendra D.; Jutras, Brandon L.; Rutkowski, Melanie R.; Pires, Marcos M. (American Chemical Society, 2024-04-09)
The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activates peptidoglycan sensors in human cells, including the nucleotide-binding oligomerization domain-containing protein 2. When present in the gastrointestinal tract, both the polymeric form (sacculi) and depolymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth. To utilize this growing area of biology toward therapeutic prescriptions, it will be critical to directly analyze a key feature of the host-microbiome interaction from living hosts in a reproducible and noninvasive way. Here we show that metabolically labeled peptidoglycan/sacculi can be readily isolated from fecal samples collected from both mice and humans. Analysis of fecal samples provided a noninvasive route to probe the gut commensal community including the metabolic synchronicity with the host circadian clock. Together, these results pave the way for noninvasive diagnostic tools to interrogate the causal nature of peptidoglycan in host health and disease.
Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F430 Modifications
Poleto, Marcelo D.; Allen, Kylie D.; Lemkul, Justin A. (American Chemical Society, 2024-06-24)
Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F-430, a nickel-containing tetrahydrocorphin. Several modified versions of F-430 have been discovered, including the 17(2)-methylthio-F-430 (mtF(430)) used by ANME-1 MCR. Here, we employ molecular dynamics (MD) simulations to investigate the active site dynamics of MCR from Methanosarcina acetivorans and ANME-1 when bound to the canonical F-430 compared to 17(2)-thioether coenzyme F-430 variants and substrates (methyl-coenzyme M and coenzyme B) for methane formation. Our simulations highlight the importance of the Gln to Val substitution in accommodating the 17(2) methylthio modification in ANME-1 MCR. Modifications at the 17(2) position disrupt the canonical substrate positioning in M. acetivorans MCR. However, in some replicates, active site reorganization to maintain substrate positioning suggests that the modified F-430 variants could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields that are pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the importance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active site dynamics, the enzyme's organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics.
Kinetic Characterization and Identification of Key Active Site Residues of the L-Aspartate N-Hydroxylase, CreE
Johnson, Sydney B.; Valentino, Hannah; Sobrado, Pablo (Wiley-V C H Verlag, 2024-07-15)
CreE is a flavin-dependent monooxygenase (FMO) that catalyzes three sequential nitrogen oxidation reactions of L-aspartate to produce nitrosuccinate, contributing to the biosynthesis of the antimicrobial and antiproliferative nautral product, cremeomycin. This compound contains a highly reactive diazo functional group for which the reaction of CreE is essential to its formation. Nitro and diazo functional groups can serve as potent electrophiles, important in some challenging nucleophilic addition reactions. Formation of these reactive groups positions CreE as a promising candidate for biomedical and synthetic applications. Here, we present the catalytic mechanism of CreE and the identification of active site residues critical to binding L-aspartate, aiding in future enzyme engineering efforts. Steady-state analysis demonstrated that CreE is very specific for NADPH over NADH and performs a highly coupled reaction with L-aspartate. Analysis of the rapid-reaction kinetics showed that flavin reduction is very fast, along with the formation of the oxygenating species, the C4a-hydroperoxyflavin. The slowest step observed was the dehydration of the flavin. Structural analysis and site-directed mutagenesis implicated T65, R291, and R440 in the binding L-aspartate. The data presented describes the catalytic mechanism and the active site architecture of this unique FMO.
Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer
Montgomery, Julia M.; Lemkul, Justin A. (American Chemical Society, 2024-07-22)
The cell membrane functions as a semipermeable barrier that governs the transport of materials into and out of cells. The bilayer features a distinct dielectric gradient due to the amphiphilic nature of its lipid components. This gradient influences various aspects of small molecule permeation and the folding and functioning of membrane proteins. Here, we employ polarizable molecular dynamics simulations to elucidate the impact of the electronic environment on the permeation process. We simulated eight distinct amino-acid side chain analogs within a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer using the Drude polarizable force field (FF). Our approach includes both unbiased and umbrella sampling simulations. By using a polarizable FF, we sought to investigate explicit dipole responses in relation to local electric fields along the membrane normal. We evaluate molecular dipole moments, which exhibit variation based on their localization within the membrane, and compare the outcomes with analogous simulations using the nonpolarizable CHARMM36 FF. This comparative analysis aims to discern characteristic differences in the free energy surfaces of permeation for the various amino-acid analogs. Our results provide the first systematic quantification of the impact of employing an explicitly polarizable FF in this context compared to the fixed-charge convention inherent to nonpolarizable FFs, which may not fully capture the influence of the membrane dielectric gradient.
Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast
Chaisupa, Patarasuda; Rahman, Md Mahbubur; Hildreth, Sherry B.; Moseley, Saede; Gatling, Chauncey; Bryant, Matthew R.; Helm, Richard F.; Wright, R. Clay (American Chemical Society, 2024-08-28)
Auxins are crucial signaling molecules that regulate the growth, metabolism, and behavior of various organisms, most notably plants but also bacteria, fungi, and animals. Many microbes synthesize and perceive auxins, primarily indole-3-acetic acid (IAA, referred to as auxin herein), the most prevalent natural auxin, which influences their ability to colonize plants and animals. Understanding auxin biosynthesis and signaling in fungi may allow us to better control interkingdom relationships and microbiomes from agricultural soils to the human gut. Despite this importance, a biological tool for measuring auxin with high spatial and temporal resolution has not been engineered in fungi. In this study, we present a suite of genetically encoded, ratiometric, protein-based auxin biosensors designed for the model yeast Saccharomyces cerevisiae. Inspired by auxin signaling in plants, the ratiometric nature of these biosensors enhances the precision of auxin concentration measurements by minimizing clonal and growth phase variation. We used these biosensors to measure auxin production across diverse growth conditions and phases in yeast cultures and calibrated their responses to physiologically relevant levels of auxin. Future work will aim to improve the fold change and reversibility of these biosensors. These genetically encoded auxin biosensors are valuable tools for investigating auxin biosynthesis and signaling in S. cerevisiae and potentially other yeast and fungi and will also advance quantitative functional studies of the plant auxin perception machinery, from which they are built.
Age-related dysregulation of proteasome-independent K63 polyubiquitination in the hippocampus and amygdala
Bae, Yeeun; Venkat, Harshini; Preveza, Natalie; Ray, W. Keith; Helm, Richard F.; Jarome, Timothy J. (Pergamon-Elsevier, 2025-08-06)
Cognitive decline with aging is a complex process involving multiple brain regions and molecular mechanisms. While the role of the canonical protein degradation function of the ubiquitin–proteasome system (UPS) has been well studied in the context of aging and age-associated memory loss, the non-proteolytic functions of ubiquitin activity remain poorly understood. Here, we investigated the role of lysine-63 (K63) polyubiquitination, the most abundant form of proteasome-independent ubiquitination, in aged rats, focusing on the hippocampus and amygdala, two brain regions reported to have cellular and molecular alterations with age that are associated with age-related memory loss. Using an unbiased proteomic approach, we observed a significant increase of K63 polyubiquitination in the hippocampus across the lifespan. Reducing K63 polyubiquitination in the hippocampus of aged male rats using the CRISPR-dCas13 RNA editing system enhanced contextual fear memory, while similar manipulations in middle-aged rats, which typically have normal memory, had no effect, emphasizing the age-dependent role of K63 polyubiquitination in memory formation. Conversely, the amygdala showed a consistent reduction of K63 polyubiquitination protein targets across the lifespan, and further reductions of K63 polyubiquitination improved memory retention in aged, but not middle-aged, male rats. Together, our findings reveal the dynamic and region-specific functions of K63 polyubiquitination in the brain aging process, providing novel insights into its contribution to age-associated memory decline.
Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations
Poleto, Marcelo D.; Lemkul, Justin A. (American Chemical Society, 2024-11-08)
The environmental and economic challenges posed by the widespread use and disposal of plastics, particularly poly(ethylene terephthalate) (PET), require innovative solutions to mitigate their impact. Such mitigation begins with understanding physical properties of the polymer that could enable new recycling technologies. Although molecular simulations have provided valuable insights into PET interactions with various PET hydrolases, current nonpolarizable force fields neglect the electronic polarization effects inherent to PET interactions. Here, we present parameters for PET polymer and its derivatives that are compatible with the Drude polarizable force field. Our parameter fitting protocol accurately reproduces electrostatic properties from quantum mechanical calculations. We then studied electronic properties of PET amorphous slabs and PET crystal units, revealing a crucial electronic polarization response of PET residues at the interface with water or vacuum, yielding insights into the modulation of electrostatic properties by solvent molecules. Finally, we showcase the interaction between a carbohydrate-binding protein and the PET crystal unit, revealing the role of electronic polarization in enhancing binding affinity. This study represents the first extension of the Drude polarizable force field to a synthetic polymer, offering a robust tool for exploring PET material properties and advancing the design of efficient (bio)technologies for addressing plastic pollution.
Using native and synthetic genes to disrupt inositol pyrophosphates and phosphate accumulation in plants
Freed, Catherine; Craige, Branch; Donahue, Janet; Cridland, Caitlin; Williams, Sarah Phoebe; Pereira, Chris; Kim, Jiwoo; Blice, Hannah; Owen Jr, James; Gillaspy, Glenda (Oxford University Press, 2024-11-26)
Inositol pyrophosphates are eukaryotic signaling molecules that have been recently identified as key regulators of plant phosphate sensing and homeostasis. Given the importance of phosphate to current and future agronomic practices, we sought to design plants, which could be used to sequester phosphate, as a step in a phytoremediation strategy. To achieve this, we expressed diadenosine and diphosphoinositol polyphosphate phosphohydrolase (DDP1), a yeast (Saccharomyces cerevisiae) enzyme demonstrated to hydrolyze inositol pyrophosphates, in Arabidopsis thaliana and pennycress (Thlaspi arvense), a spring annual cover crop with emerging importance as a biofuel crop. DDP1 expression in Arabidopsis decreased inositol pyrophosphates, activated phosphate starvation response marker genes, and increased phosphate accumulation. These changes corresponded with alterations in plant growth and sensitivity to exogenously applied phosphate. Pennycress plants expressing DDP1 displayed increases in phosphate accumulation, suggesting that these plants could potentially serve to reclaim phosphate from phosphate-polluted soils. We also identified a native Arabidopsis gene, Nucleoside diphosphate-linked moiety X 13 (NUDIX13), which we show encodes an enzyme homologous to DDP1 with similar substrate specificity. Arabidopsis transgenics overexpressing NUDIX13 had lower inositol pyrophosphate levels and displayed phenotypes similar to DDP1-overexpressing transgenics, while nudix13-1 mutants had increased levels of inositol pyrophosphates. Taken together, our data demonstrate that DDP1 and NUDIX13 can be used in strategies to regulate plant inositol pyrophosphates and could serve as potential targets for engineering plants to reclaim phosphate from polluted environments.
Highly Active Oligoethylene Glycol Pleuromutilins via Systematic Linker Synthesis/One-Pot Attachment and a Microscale Solubility Method
Breiner, Logan M.; Slowinski, Roman P.; Lowell, Andrew N. (American Chemical Society, 2024-12-18)
The semisynthetic derivatization of natural products is crucial for their continued development as antibiotics. While commercial pleuromutilin derivatives depend on amines for solubility, we demonstrate the high activity and solubility of oligoethylene glycol-substituted pleuromutilins achieved via a one-pot deprotection/attachment approach using thiolates protected as thioesters. The bifunctional linker synthesis is versatile and can be broadly applied to other chemistries. Antibacterial assays revealed this simple glycolate modification enhanced inhibition 4-8-fold relative to that of pleuromutilin. A new microscale solubility method is also introduced.
Differential elimination of marked sex chromosomes enables production of nontransgenic male mosquitoes in a single strain
Compton, Austin; Sharma, Atashi; Hempel, Melanie; Aryan, Azadeh; Biedler, James K.; Potters, Mark B.; Chandrasegaran, Karthikeyan; Vinauger, Clément; Tu, Zhijian (National Academy of Sciences, 2025-05-08)
Diverse genetic strategies are being pursued to control mosquito-borne infectious diseases. These strategies often rely on the release of nonbiting males to either reduce the target mosquito population or render them resistant to pathogens. Male-only releases are important as any contaminating females can bite and potentially transmit pathogens. Despite significant efforts, it remains a major bottleneck to reliably and efficiently separate males from females, especially when nontransgenic males are preferred. In the yellow fever mosquito Aedes aegypti, sex is determined by a pair of homomorphic sex chromosomes, with the dominant male-determining locus (the M locus) and its counterpart (the m locus) embedded in an M-bearing and an m-bearing chromosome 1, respectively. We utilized both naturally occurring and engineered sex-linked recessive lethal alleles (RLAs) to create sex separation strains for Ae. aegypti on the basis of differential elimination of marked sex chromosomes (DeMark). DeMark strains are self-sustaining and produce nontransgenic males that are readily separated from individuals carrying RLA-and transgene-marked m chromosomes. For example, the marked m chromosome in the heterozygous mother in some strains was only inherited by her female progeny due to RLA-mediated incompatibility with the M-bearing chromosome in the father, producing nontransgenic males and transgenic females, generation after generation. We further explore strategies to conditionally eliminate females that contain marked sex chromosomes. We also discuss DeMark designs that are applicable for efficient sex separation in organisms with well-differentiated X and Y chromosomes, such as the Anopheles mosquitoes.
Amino Acid Biostimulants Enhance Drought and Heat Stress Tolerance of Creeping Bentgrass (Agrostis Stolonifera L.)
Zhang, Xunzhong; Goatley, J. Michael Jr.; Focke, Maude; Sherman, Graham; Smith, Berit; Motsinger, Taylor; Roué, Catherine; Goos, Jay (MDPI, 2025-07-19)
Creeping bentgrass (Agrostis stolonifera L.) is an important cool-season turfgrass species widely used for golf course putting greens; however, it experiences a summer stress-induced quality decline in the U.S. transition zone and other regions with similar climates. The objective of this study was to determine the effects of five amino acid biostimulants on creeping bentgrass drought and heat stress tolerance. The five biostimulants, including Superbia, Amino Pro V, Siapton, Benvireo, and Surety, at the rate of 0.22 g of N m⁻², were applied biweekly to foliage, and the treatments were arranged in a randomized block design with four replications and were subjected to 56 days of heat and drought stress in growth chamber conditions. The amino acid biostimulants Superbia and Amino Pro V improved the turf quality, photochemical efficiency (PE), normalized difference vegetation index (NDVI), chlorophyll content, antioxidant enzyme superoxide dismutase activity, root growth, and viability and suppressed leaf H₂O₂ levels when compared to a control. Among the treatments, Superbia and Amino Pro V exhibited greater beneficial effects on turf quality and physiological fitness. The results of this study suggest that foliar application of amino acid biostimulants may improve the summer stress tolerance of cool-season turfgrass species in the U.S. transition zone and other regions with similar climates.
Larval environment reshapes mosquito disease risk via phenotypic and molecular plasticity
Chandrasegaran, Karthikeyan; Walker, Melody; Marano, Jeffrey M.; Rami, Spruha; Bisese, Adaline; Weger-Lucarelli, James; Lahondère, Chloé; Robert, Michael A.; Childs, Lauren M.; Vinauger, Clément (2025-06-21)
Early-life environmental conditions can exert profound, lasting effects on adult phenotypes, with major consequences for fitness and disease transmission, especially in holometabolous insects like mosquitoes, which are a key vector species. Yet, the molecular mechanisms through which juvenile environments shape adult physiology and behavior via transstadial effects remain largely unresolved. Here, we demonstrate that larval competition, a key ecological stressor, profoundly alters adult body size, survival, reproductive output, host-seeking behavior, olfactory neurophysiology, and vector competence in the mosquito Aedes aegypti. Crucially, using transcriptomic profiling and integrative network analyses, we identify seven regulatory hub genes whose expression is strongly associated with size-dependent variation in olfactory behavior, reproductive investment, and Zika virus transmission potential. These hub genes belong to gene modules enriched for functions in chemosensory processing, metabolic regulation, and signal transduction, revealing a molecular framework mediating environmentally induced plasticity across metamorphosis. Integrating these empirical findings into a transmission model, we show that incomplete larval control can inadvertently increase outbreak risk by producing larger, longer-lived, and more competent vectors. Our results uncover molecular mechanisms underpinning phenotypic plasticity in disease vectors and highlight the critical need to account for transstadial effects in models of vector-borne disease transmission.
Case Study: Genetic and In Silico Analysis of Familial Pancreatitis
Sharma, Yash; Good, Deborah J. (MDPI, 2025-05-20)
Background/Objectives: Chronic pancreatitis (CP) is a progressive inflammatory condition of the pancreas that leads to irreversible changes in pancreatic structure. The pancreatic α and β cells secrete hormones such as insulin and glucagon into the bloodstream. The pancreatic acinar cells secrete digestive enzymes that break down macromolecules. When these digestive enzymes do not function properly, maldigestion, malabsorption, and malnutrition may result. Presented here is a case study of an individual newly diagnosed with chronic pancreatitis, along with a genetic analysis of his son and an in-silico analysis of two of the variant proteins. Methods: This study was conducted using human subjects, namely, the proband (father) and his son. Medical genetic testing of the proband (father) identified the presence of two variants in the cystic fibrosis transmembrane receptor gene (CFTR): variant rs213950, resulting in a single amino acid change (p. Val470Met), and variant rs74767530, a nonsense variant (Arg1162Ter) with known pathogenicity for cystic fibrosis. Medical testing also revealed an additional missense variant, rs515726209 (Ala73Thr), in the CTRC gene. Cheek cell DNA was collected from both the proband and his son to determine the inheritance pattern and identify any additional variants. A variant in the human leukocyte antigen (rs7454108), which results in the HLA-DQ8 haplotype, was examined in both the proband and his son due to its known association with autoimmune disease, a condition also linked to chronic pancreatitis. In silico tools were subsequently used to examine the impact of the identified variants on protein function. Results: Heterozygosity for all variants originally identified through medical genetic testing was confirmed in the proband and was absent in the son. Both the proband and his son were found to have the DRB1*0301 (common) haplotype for the HLA locus. However, the proband was also found to carry a linked noncoding variant, rs2647088, which was absent in the son. In silico analysis of variant rs213950 (Val470Met) in CFTR and rs515726209 (Ala73Thr) in CTRC revealed distinct changes in predicted ligand binding for both proteins, which may affect protein function and contribute to the development of CP. Conclusions: This case study of a proband and his son provides additional evidence for a polygenic inheritance pattern in CP. The results also highlight new information on the role of the variants on protein function, suggesting additional testing of ligand binding for these variants should be done to confirm the functional impairments.
Evolution at Spike protein position 519 in SARS-CoV-2 facilitated adaptation to humans
Cereghino, C.; Michalak, K.; DiGiuseppe, S.; Yu, D.; Faraji, A.; Sharp, A.K.; Brown, Anne M.; Kang, L.; Weger-Lucarelli, James; Michalak, P. (Springer Nature, 2024)
As the COVID-19 pandemic enters its fourth year, the pursuit of identifying a progenitor virus to SARSCoV- 2 and understanding the mechanism of its emergence persists, albeit against the backdrop of intensified efforts to monitor the ongoing evolution of the virus and the influx of new mutations. Surprisingly, few residues hypothesized to be essential forSARS-CoV-2 emergence and adaptation to humans have been validated experimentally, despite the importance that these mutations could contribute to the development of effective antivirals. To remedy this,we searched for genomic regions in the SARS-CoV-2 genome that show evidence of past selection around residues unique to SARSCoV- 2 compared with closely related coronaviruses. In doing so, we identified a residue at position 519 in Spike within the receptor binding domain that holds a static histidine in human-derived SARSCoV- 2 sequences but an asparagine in SARS-related coronaviruses from bats and pangolins. In experimental validation, the SARS-CoV-2 Spike protein mutant carrying the putatively ancestral H519N substitution showed reduced replication in human lung cells, suggesting that the histidine residue contributes to viral fitness in the human host. Structural analyses revealed a potential role of Spike residue 519 in mediating conformational transitions necessary for Spike prior to binding with ACE2. Pseudotyped viruses bearing the putatively ancestral N519 also demonstrated significantly reduced infectivity in cells expressing the human ACE2 receptor compared to H519. ELISA data corroborated that H519 enhances Spike binding affinity to the human ACE2 receptor compared to the putatively ancestral N519. Collectively, these findings suggest that the evolutionary transition at position 519 of the Spike protein played a critical role inSARS-CoV-2 emergence and adaptation to the human host. Additionally, this residue presents as a potential drug target for designing small molecule inhibitors tailored to this site.
Indirectly acquired fear memories have distinct, sex-specific molecular signatures from directly acquired fear memories
Navabpour, Shaghayegh; Patrick, Morgan B.; Omar, Nour A.; Kincaid, Shannon E.; Bae, Yeeun; Abraham, Jennifer; McGrew, Jacobi; Musaus, Madeline; Ray, W. Keith; Helm, Richard F.; Jarome, Timothy J. (PLOS, 2024-12-23)
Post-traumatic stress disorder (PTSD) is a severe anxiety disorder that affects women more than men. About 30% of patients suffering from PTSD develop the disorder by witnessing a traumatic event happen to someone else. However, as the focus has remained on those directly experiencing the traumatic event, whether indirectly acquired fear memories that underlie PTSD have the same molecular signature as those that are directly acquired remains unknown. Here, using a rodent indirect fear learning paradigm where one rat (observer) watches another rat (demonstrator) associate an auditory cue with foot shock, we found that fear can be indirectly acquired by both males and females regardless of the sex or novelty (familiarity) of the demonstrator animal. However, behaviorally, indirectly acquired fear responses resemble those of pseudoconditioning, a behavioral response that is thought to not represent learning. Despite this, using unbiased proteomics, we found that indirectly acquired fear memories have distinct protein degradation profiles in the amygdala and anterior cingulate cortex (ACC) relative to directly acquired fear memories and pseudoconditioning, which further differed significantly by sex. Additionally, Egr2 and c-fos expression in the retrosplenial cortex of observer animals resembled that of demonstrator rats but was significantly different than that of pseudoconditioned rats. Together, these findings reveal that indirectly acquired fear memories have sex-specific molecular signatures that differ from those of directly acquired fear memories or pseudoconditioning. These data have important implications for understanding the neurobiology of indirectly acquired fear memories that may underlie bystander PTSD.
Evaluation of ebony as a potential selectable marker for genetic sexing in Aedes aegypti
Nikolouli, Katerina; Compton, Austin; Tu, Zhijian J.; Bourtzis, Kostas (2025-02-25)
Background: Aedes aegypti is expected to invade previously unoccupied areas, mainly due to the climate change, the increase in travel and trade activities and the continuous transformation of the rural environment into urban areas. The sterile insect technique (SIT), which relies on the mass production and release of sterile males, is an environmentally friendly approach that can be applied for population control of Ae. aegypti. SIT programs can be greatly benefited by a genetic sexing strain (GSS) and a reliable sex sorting system to minimize any accidental female release. Visually detectable or conditionally lethal selectable markers can be used for the development of new GSSs. In this study, we evaluated the suitability and competence of a mutant Ae. aegypti ebony strain for the development of a new GSS. The ebony gene is known to be involved in the pigmentation pathway of several dipteran insects, including Ae. aegypti. Methods: An ebony gene knockout was developed though CRISPR/Cas9 mutagenesis. G0 individuals with the desired phenotype were crossed, and progeny were screened in every generation. PCR and sequencing were performed using gDNA from a pulled leg to determine the mutant genotype. Quality control tests, including pupae and adult recovery rates, male sex ratio and fecundity, were applied to the ebony mutant line to determine whether the mutation confers any fitness cost. Results: An Ae. aegypti ebony knockout mutant carrying a 5-bp deletion was obtained, which presented darker head and siphon phenotypes at the larval stage. However, genetic analysis revealed that this ebony mutation results in incomplete penetrance and variable expressivity. The establishment of a pure ebony mutant line was not possible because of the fitness costs conferred by the mutation. Conclusions: In this study, the adequacy and suitability of the ebony gene as a selectable marker for the development of a GSS in Ae. aegypti were assessed. Despite its clear phenotype early in larval development, the homozygous mutant line presented phenotypic inconsistency and loss of fertility. These drawbacks clearly indicate that this particular mutation is not suitable for the development of a new GSS. Nonetheless, it cannot be excluded that a different mutation will lead to a different expression and penetrance profile and a viable homozygous mutant line.
Identification of small molecule inhibitors of the Chloracidobacterium thermophilum type IV pilus protein PilB by ensemble virtual screening
McDonald-Ramos, Jay S.; Hicklin, Ian K.; Yang, Zhaomin; Brown, Anne M. (Elsevier, 2024-08-16)
Antivirulence strategy has been explored as an alternative to traditional antibiotic development. The bacterial type IV pilus is a virulence factor involved in host invasion and colonization in many antibiotic resistant pathogens. The PilB ATPase hydrolyzes ATP to drive the assembly of the pilus filament from pilin subunits. We evaluated Chloracidobacterium thermophilum PilB (CtPilB) as a model for structure-based virtual screening by molecular docking and molecular dynamics (MD) simulations. A hexameric structure of CtPilB was generated through homology modeling based on an existing crystal structure of a PilB from Geobacter metallireducens. Four representative structures were obtained from molecular dynamics simulations to examine the conformational plasticity of PilB and improve docking analyses by ensemble docking. Structural analyses after 1 μs of simulation revealed conformational changes in individual PilB subunits are dependent on ligand presence. Further, ensemble virtual screening of a library of 4234 compounds retrieved from the ZINC15 database identified five promising PilB inhibitors. Molecular docking and binding analyses using the four representative structures from MD simulations revealed that top-ranked compounds interact with multiple Walker A residues, one Asp-box residue, and one arginine finger, indicating these are key residues in inhibitor binding within the ATP binding pocket. The use of multiple conformations in molecular screening can provide greater insight into compound flexibility within receptor sites and better inform future drug development for therapeutics targeting the type IV pilus assembly ATPase.

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