Biology subjects

Tripathi, B.

Publications and source records attributed to Tripathi, B..

4 recordsLinked to original sources

bioRxiv2025

eIF2B Selectively Anchors and Activates Mutant KRAS

Much is known about how RAS oncoproteins regulate mRNA translation factors, but the reverse relationship, how translation factors influence RAS activity, has remained largely unexplored. At the plasma membrane (PM), Son of Sevenless (SOS) acts as the canonical guanine nucleotide exchange factor (GEF) for RAS proteins, yet mechanisms governing its specificity for individual RAS isoforms remain unknown. Here, we show that the translation initiation factor eIF2B, best known for its GEF function in translation initiation, forms a distinct complex with SOS and mutant KRAS at the PM, but not with other oncogenic RAS variants. Mechanistically, eIF2B acts as an allosteric regulator of SOS, selectively enhancing GDP-GTP exchange on mutant KRAS. This specificity arises from the translational activity of eIF2B, which upregulates glycosphingolipid (GSL) biosynthesis to remodel PM lipids and preferentially anchor mutant KRAS. Together, our results uncover an unexpected moonlighting function of eIF2B: acting both as a direct activator of SOS and as a regulator of GSL pathway that shapes the membrane landscape, both required for mutant KRAS activation. These insights redefine our understanding of eIF2B and mutant KRAS functions in cancer and have profound implications for KRAS-driven oncogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/686860v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1f50934org.highwire.dtl.DTLVardef@2f55b9org.highwire.dtl.DTLVardef@1a51e39org.highwire.dtl.DTLVardef@1634aac_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIeIF2B interacts with mutant KRAS and SOS at the plasma membrane (PM). C_LIO_LIThe eIF2B:SOS complex promotes the GTP-bound active state of mutant KRAS. C_LIO_LIeIF2B enhances the translation of B4GALT5 mRNA, encoding a key enzyme of glycosphingolipid (GSL) biosynthesis. C_LIO_LIUpregulation of the GSL metabolites, ganglioside GM3 and sulfatide SM4, remodels PM lipid composition to facilitate eIF2B:SOS:KRAS complex formation and mutant KRAS nanoclustering. C_LIO_LIThrough its interaction with SOS and stimulation of GSL synthesis, eIF2B selectively activates mutant KRAS at the PM among RAS isoforms. C_LIO_LIeIF2B is required for the development of mKRAS-driven lung adenocarcinoma in mice. C_LIO_LIeIF2B is a marker of poor prognosis in mutant KRAS-driven cancers. C_LI

cancer biology↗

bioRxiv2025

Dachsous-Fat Signaling Shapes the Drosophila Wing through Mechanical Forces

Proper organ shape is critical for function. The Drosophila wing normally adopts an elongated shape, but mutations in the Dachsous-Fat pathway result in rounder wings. The mechanism by which this occurs has remained unclear. Here, we show that Ds-Fat signaling shapes the wing during the larval stage, rather than during pupal development when morphogenetic rearrangements transform the developing wing disc into the adult wing. We further find that Ds-Fat alters tissue wide stresses in the wing disc, and genetic manipulations that reduce cytoskeletal tension result in rounder wings, whereas increasing cytoskeletal tension produces more elongated wings. Reduced tension is also associated with less oriented growth during development. Notably, increased cytoskeletal tension partially rescues the rounder shape caused by ds knockdown. These results reveal a previously unrecognized mechanism by which Ds-Fat signaling determines wing shape, involving regulation of tissue tension to orient growth and shape the wing primordia during larval development.

developmental biology↗

bioRxiv2025

Internal DNA standards for Isopycnic Centrifugation of Environmental DNA in Quantitative Stable Isotope Probing

Element assimilation rates or the DNA replication rate of microbial taxa can be measured in environmental samples through quantitative DNA-stable isotope probing (DNA-qSIP). Here, we introduce a set of DNA standards that may be used to quantify the density of DNA extracted from environmental samples after isopycnic centrifugation. The standards are approximately 9 Kbp PCR products with either isotopically enriched (98 atom% 15N, 13C) nucleotides or natural abundance nucleotides and have densities that differ by 0.051 g/mL. The internal standards were tested in a DNA-qSIP analysis of bacterial populations in soil exposed to 63 atom% H218O, performed in two different laboratories with different equipment and protocols. While fractionation results, including number of fractions taken and differences in density between adjacent fractions, between the two laboratories were different, the internal standards allowed the two data sets to be compared, and both research groups found similar Excess Atom Fraction (EAF) of oxygen-18 in the DNA of bacterial taxa. These internal DNA standards allow direct comparison of DNA-qSIP results from different experiments regardless of operator, tracer enrichment levels, protocol or equipment used and can support the creation of a large global database that contains qSIP results from many different laboratories. ImportanceDNA-qSIP is an important technique in microbial ecology that allows the growth and nutrient assimilation rates of microbial taxa, including those that have not yet been cultured, to be measured. Growth and assimilation rates are extremely variable parameters in microbial ecology because most of the microbial community is dormant and inactive, which complicates linking microbial populations to ecosystem processes. DNA-qSIP is increasingly practiced in a range of laboratories, using different equipment, isotopes, substrates, and protocols, making comparison of results among different research groups challenging. Here we describe the development of internal standards, 2 pieces of DNA with different isotopic content and hence buoyant density, that can be added to environmental DNA before isopycnic centrifugation. Our results show the internal DNA standards allow DNA-qSIP results to be compared across laboratories and could contribute to the formation of a large DNA-qSIP database that contains growth or nutrient assimilation rates of microbial taxa from many different experiments.

microbiology↗

bioRxiv2021

Wild pigs mediate far-reaching agricultural impacts on tropical forest soil microbial communities

Edge effects, the altered abiotic and biotic conditions on the borders of natural areas, rarely extend more than a few hundred meters. Edge effects have rarely been linked to altered soil biota, which shape ecosystem processes including carbon storage, biogeochemical cycling, and plant performance. Here, we investigated if agriculturally-mediated increased wildlife populations affect soil biotic communities at a distance well over that of estimated edge effects when they move between agriculture and natural habitats using a 22-year fenced exclusion experiment in a primary rainforest in Peninsular Malaysia. We found that the presence of wildlife (mainly native pigs (Sus scrofa) that crop-raid in nearby oil palm plantations) was associated with higher bacterial diversity, and an altered community composition (mediated by changes in soil pH), and reduced abundances of symbiotic ectomycorrhizal fungi compared to soil in exclosures. There were only minor effects of pigs on soil chemistry or microclimate, so we suggest that changes in soil communities are driven by pigs leaf litter removal and alterations to plant composition. Our study highlights that indirect effects from agriculture can be transferred by wildlife >1 km into protected areas and this could have important repercussions for ecosystem processes and plant-soil feedbacks.

ecology↗