Biology subjects

Walker, E. L.

Publications and source records attributed to Walker, E. L..

6 recordsLinked to original sources

bioRxiv2024

Structural Convergence and Water-Mediated Substrate Mimicry Enable Broad Neuraminidase Inhibition by Human Antibodies

Influenza has been responsible for multiple global pandemics and seasonal epidemics and claimed millions of lives. The imminent threat of a panzootic outbreak of avian influenza H5N1 virus underscores the urgent need for pandemic preparedness and effective countermeasures, including monoclonal antibodies (mAbs). Here, we characterize human mAbs that target the highly conserved catalytic site of viral neuraminidase (NA), termed NCS mAbs, and the molecular basis of their broad specificity. Cross-reactive NA-specific B cells were isolated by using stabilized NA probes of non-circulating subtypes. We found that NCS mAbs recognized multiple NAs of influenza A as well as influenza B NAs and conferred prophylactic protections in mice against H1N1, H5N1, and influenza B viruses. Cryo-electron microscopy structures of two NCS mAbs revealed that they rely on structural mimicry of sialic acid, the substrate of NA, by coordinating not only amino acid side chains but also water molecules, enabling inhibition of NA activity across multiple influenza A and B viruses, including avian influenza H5N1 clade 2.3.4.4b viruses. Our results provide a molecular basis for the broad reactivity and inhibitory activity of NCS mAbs targeting the catalytic site of NA through substrate mimicry.

immunology↗

bioRxiv2024

Strigolactones are involved in enhancing iron uptake in maize

Strigolactones are plant hormones with roles in a wide range of signaling and developmental processes. A yellow-striped maize mutant, (interveinal yellow) ivy, was determined to have low iron in tissues under normal growth conditions. The gene underlying the ivy mutation was mapped and identified as ZmCCD8, a key enzyme in the biosynthesis of strigolactones. Under iron-replete conditions, comparison of the transcriptomes of wild-type plants and maize ccd8 mutants revealed suppression of several iron-regulated genes in ccd8. These genes are normally up-regulated during iron deficiency and include the key iron-regulated transcription factor IRO2 as well as genes involved in the biosynthesis of iron chelators and transporters. External supply of synthetic strigolactone to ivy mutants alleviated chlorosis and returned iron-regulated gene expression to wild-type levels. In iron limited conditions, iron-regulated gene expression in ccd8 mutants responded normally, indicating that strigolactones are not required for response to externally imposed iron deficiency. However, they are required for basal expression of iron-regulated genes when adequate iron is available, highlighting a distinction between iron homeostasis during normal growth, and the iron deficiency response triggered by the lack of external available iron. The connection between strigolactones and iron homeostasis is not limited to maize, as Arabidopsis ccd8 mutants also show strong chlorosis when grown on medium with moderate levels of iron. This previously unappreciated role may have implications for the use of strigolactones in agricultural contexts.

plant biology↗

bioRxiv2023

The small RNA component of Arabidopsis phloem sap and its response to iron deficiency.

In order to discover sRNA that might function during iron deficiency stress, RNA was prepared from phloem exudates of Arabidopsis thaliana. Bioanalyzer results indicate that abundant RNA from phloem is small in size--less than 200 nt. Moreover, typical rRNA bands were not observed. Sequencing of eight independent phloem RNA samples indicated that that tRNA-derived fragments, specifically 5 tRFs and 5 tRNA halves, are highly abundant in phloem sap, comprising about 46% of all reads. In addition, a set of miRNAs that are present in phloem sap was defined, and several miRNA and sRNAs were identified that are differentially expressed during iron deficiency. HighlightPreparation of RNA from Arabidopsis phloem sap revealed that O_LImost of the RNA is small (less than 200 nt) C_LIO_LItRNA fragments (tRFs) are highly abundant C_LIO_LIa set of miRNAs present in phloem sap can be defined C_LI

plant biology↗

bioRxiv2022

CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana

Long non-coding RNAs (lncRNAs) are RNA molecules with functions independent of any protein-coding potential. A whole transcriptome (RNA-seq) study of Arabidopsis shoots under iron sufficient and deficient conditions was carried out to determine the genes that are iron-regulated in the shoots. We identified two previously unannotated transcripts on chromosome 1 that are significantly iron-regulated. We have called this iron-regulated lncRNA, CAN OF SPINACH (COS). cos mutants have altered iron levels in leaves and seeds. Despite the low iron levels in the leaves, cos mutants have higher chlorophyll levels than WT plants. Moreover, cos mutants have abnormal development during iron deficiency. Roots of cos mutants are longer than those of WT plants, when grown on iron deficient medium. In addition, cos mutant plants accumulate singlet oxygen during iron deficiency. The mechanism through which COS affects iron deficiency responses is unclear, but small regions of sequence similarity to several genes involved in iron deficiency responses occur in COS, and small RNAs from these regions have been detected. We hypothesize that COS is required for normal adaptation to iron deficiency conditions.

plant biology↗

bioRxiv2021

OPT3 plays a central role in both copper and iron homeostasis and signaling due to its ability to deliver copper as well as iron to the phloem in Arabidopsis

Copper and iron are essential micronutrients but are toxic when accumulating in cells in excess. Thus, their uptake by roots is tightly regulated. While plants sense and respond to local copper availability, the systemic regulation of copper uptake has not been documented. By contrast, both local and systemic control for iron uptake has been reported. Iron abundance in the phloem has been suggested to act systemically, regulating the expression of iron uptake genes in the root. Consistently, shoot-to-root iron signaling is disrupted in A. thaliana mutants lacking the phloem companion cell-localized iron transporter, AtOPT3: opt3 mutants overaccumulate iron in leaves while constitutively upregulating iron deficiency-responsive genes in roots. We report that AtOPT3 transports copper and mediates its delivery from source leaves to sinks including young leaves and developing embryos. Consequently, the opt3 mutant accumulates less copper in the phloem, is sensitive to copper deficiency, and mounts transcriptional copper deficiency response in roots. Copper rescues these defects. Notably, feeding the opt3 mutant with copper or iron via the phloem in leaves downregulates the expression of both copper and iron-deficiency marker genes in roots, suggesting that copper and iron can substitute each others function in the phloem in shoot-to-root communication. One-sentence summaryAtOPT3 loads copper and iron into the phloem companion cells, for subsequent distribution to sink tissues and systemic signaling of copper and iron deficiency.

plant biology↗

bioRxiv2020

Medicago truncatula Yellow Stripe-Like7 encodes a peptide transporter required for symbiotic nitrogen fixation

Yellow Stripe-Like (YSL) proteins are a family of plant transporters typically involved in transition metal homeostasis. The substrate of three of the four YSL clades (clades I, II, and IV) are metal complexes with non-proteinogenic amino acid nicotianamine or its derivatives. No such transport capabilities have been shown for any member of the remaining clade (clade III), which is able to translocate short peptides across the membranes instead. The connection between clade III YSL members and metal homeostasis might have been masked by the functional redundancy characteristic of this family. This might have been circumvented in legumes through neofunctionalization of YSLs to ensure a steady supply of transition metals for symbiotic nitrogen fixation in root nodules. To test this possibility, Medicago truncatula clade III transporter MtYSL7 has been studied both when the plant was fertilized with ammonium nitrate or when nitrogen had to be provided by endosymbiotic rhizobia within the root nodules. MtYSL7 is a plasma membrane protein expressed in the vasculature and in the nodule cortex. This protein is able to transport short peptides into the cytosol, although none with known metal homeostasis roles. Reducing MtYSL7 expression levels resulted in diminished nitrogen fixation rates. In addition, nodules of mutant lines lacking YSL7 accumulated more copper and iron, the later the likely result of increased expression in roots of iron uptake and delivery genes. The available data is indicative of a role of MtYSL7, and likely other clade III YSLs, in transition metal homeostasis. ONE SENTENCE SUMMARYMedicago truncatula YSL7 is a peptide transporter required for symbiotic nitrogen fixation in legume nodules, likely controlling transition metal allocation to these organs.

plant biology↗