Biology subjects

Johnson, H. E.

Publications and source records attributed to Johnson, H. E..

6 recordsLinked to original sources

bioRxiv2025

Microbiome-host interactions drive a trade-off between sleep quality and lifespan in Drosophila

Understanding the interactions between various aging processes and the resulting heterogeneity in aging is crucial for promoting healthy aging. Here, we provide evidence that heterogeneity in microbiome and host interactions contributes to diversifying aging phenotypes in sleep, gut integrity, and longevity in Drosophila. Aged flies exhibiting sleep fragmentation preserve gut integrity, accompanied by a shift in microbiota composition, particularly an increase in Acinetobacter junii. A. junii induces sleep fragmentation via its metabolite, urocanic acid, through serotonin receptor-dependent dopamine upregulation. In parallel, A. junii exploits the host response to promote its growth, leading to lifespan extension, which is recapitulated by genetically modified Escherichia coli, suggesting a trade-off between sleep quality and lifespan. Our study demonstrates a systematic mechanism underlying aging heterogeneity, suggesting interventions through bacterial supplements.

animal behavior and cognition↗

bioRxiv2025

Optogenetic construction of de novo integrin-adhesion complexes reveals role for biocondensation in adhesion nucleation

Integrin-adhesion complexes (IACs) form spontaneously in cells on extracellular matrix substrates, allowing them to sense matrix composition and transduce force. However, IACs often do not form uniformly across a cell, which begs the question: What is required to nucleate an adhesion, and what factors enable the stabilization of an IAC once it has formed? Many factors have been suggested to promote formation and the subsequent stabilization of IACs. It is difficult to explicitly test these factors in vivo as IACs undergo constant remodeling. Here, we employ optogenetics to explicitly test the ability of talin in different activity and phase states to nucleate and stabilize IACs in regions where none are present. We find that fusion of intrinsically disordered regions directly to talin enhances its adhesion nucleation potential and allows new adhesions to be produced in response to optogenetic talin clustering. Similarly, expression of factors previously shown to enhance biocondensation in vitro, such as paxillin, the paxillin N-terminus, or unfolding of talin, allows for adhesion nucleation and biocondensation of talin. We show that these biocondensates of talin can cluster and activate integrins even in the absence of extracellular matrix. By applying optogenetic activation to regions of the cell with or without ventral actomyosin, we demonstrate actomyosin engagement promotes the formation and stability of adhesions. These results are corroborated by theoretical modelling which shows that phase separation of talin is enhanced by differential clutch formation in the presence of actomyosin thus enabling peripheral adhesion formation and stability. This work establishes a model in which increased cooperativity of talin enables IAC nucleation through talin biocondensation, which clusters and activates integrins. In addition to these findings, we generate multiple optogenetic tools that enable local nucleation or enhancement of IACs. HighlightsO_LIOptogenetic tools mediating talin biocondensation can locally induce focal adhesion formation C_LIO_LIPaxillin LD domains enable biocondensation of talin C_LIO_LIBiocondensation of talin enables IAC formation C_LIO_LIPhase separation of talin can activate integrins independently of ECM C_LIO_LIComputational model reconciles spatial variance in LLPS and IAC formation. C_LI

cell biology↗

bioRxiv2024

3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression

Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as MYC, CCND1, ETV1, CRKL, and ID4. Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including MYC, on the same complex amplicons such as ecDNA. We characterized a MYC-ERBB2 chimeric ecDNA, in which ERBB2 heavily hijacks MYCs enhancers. Notably, CRISPRi of the MYC promoter led to increased interaction of ERBB2 with MYC enhancers and elevated ERBB2 expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.

cancer biology↗

bioRxiv2023

Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo

Positional information in developing tissues often takes the form of stripes of gene expression that mark the boundaries of a particular cell type or morphogenetic process. How stripes form is still in many cases poorly understood. Here we use optogenetics and live-cell biosensors to investigate one such pattern: the posterior stripe of brachyenteron (byn) expression in the early Drosophila embryo. This byn stripe depends on interpretation of an upstream signal - a gradient of ERK kinase activity - and the expression of two target genes tailless (tll) and huckebein (hkb) that exert antagonistic control over byn. We find that high or low doses of ERK signaling produce either transient or sustained byn expression, respectively. These ERK stimuli also regulate tll and hkb expression with distinct dynamics: tll transcription is rapidly induced under both low and high stimuli, whereas hkb transcription converts graded ERK inputs into an output switch with a variable time delay. Antagonistic regulatory paths acting on different timescales are hallmarks of an incoherent feedforward loop architecture, which is sufficient to explain transient or sustained byn dynamics and adds temporal complexity to the steady-state model of byn stripe formation. We further show that an all-or-none stimulus can be blurred through intracellular diffusion to non-locally produce a stripe of byn gene expression. Overall, our study provides a blueprint for using optogenetic inputs to dissect developmental signal interpretation in space and time.

developmental biology↗

bioRxiv2019

Optogenetic rescue of a developmental patterning mutant

Animal embryos are partitioned into spatial domains by complex patterns of signaling and gene expression, yet it is still largely unknown what features of a developmental signal are essential. Part of the challenge arises because it has been impossible to \"paint\" arbitrary signaling patterns on an embryo to test their sufficiency. Here we demonstrate exactly this capability by combining optogenetic control of Ras/Erk signaling with the genetic loss of terminal signaling in early Drosophila embryos. Simple all-or-none light inputs at the embryonic termini were able to completely rescue normal development, generating viable larvae and fertile adults from this otherwise-lethal genetic mutant. Systematically varying illumination parameters further revealed that at least three distinct developmental programs are triggered by different cumulative doses of Erk. These results open the door to the targeted design of complex morphogenetic outcomes as well as the ability to correct patterning errors that underlie developmental defects.\n\nSummarySpatial gradients of protein activity pattern all developing embryos. But which features of these patterns are essential and which are dispensable for development? Answering this question has been deceptively difficult, due to the difficulty of shaping spatial gradients using chemical or genetic perturbations. Johnson and colleagues use optogenetics to fully restore normal embryo development with a pattern of light, opening the door to complete control over spatial organization in developing and engineered tissues.

developmental biology↗

bioRxiv2018

Signaling dynamics control cell fate in the early Drosophila embryo

The Erk mitogen-activated protein kinase plays diverse roles in animal development, where its activity is associated with phenomena including cell migration, proliferation and differentiation. Its widespread reuse raises a conundrum: when a single kinase like Erk is activated, how does a developing cell know which fate to adopt? Here, we combine precise optogenetic control with genetic perturbations to dissect Erk-dependent cellular responses in the early Drosophila embryo. We find that light-stimulated Erk activity is sufficient to posterior-ize the majority of the embryo, leading to massive apical constriction through expression of the autocrine receptor-ligand pair mist and fog. Ectopic contraction at non-terminal positions requires at least 1 h of high-amplitude Erk signaling, whereas a 30 min pulse of Erk activity patterns non-contractile neurogenic ectoderm during the same time window. In contrast to the canonical transient versus sustained model, the cell fate switch is triggered by the cumulative load of Erk signaling, not the duration of a single persistent pulse. Our results reveal that the early fly embryo harbors a classic example of dynamic cell fate control, where the total dose of Erk activity selects between two distinct physiological outcomes.

developmental biology↗