Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations
Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have a range of unrealized pleiotropic effects in other environments. These pleiotropic consequences of adaptation can influence the emergence of specialists or generalists, and are critical for evolution in temporally or spatially fluctuating environments. While many experiments have examined the pleiotropic effects of adaptation at a snapshot in time, very few have observed the dynamics by which these effects emerge and evolve. Here, we propagated hundreds of diploid and haploid laboratory budding yeast populations in e...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Evolutionary Biology Source Type: research

Bazooka/Par3 cooperates with Sanpodo for the assembly of Notch clusters following asymmetric division of < i > Drosophila < /i > sensory organ precursor cells
In multiple cell lineages, Delta-Notch signalling regulates cell fate decisions owing to unidirectional signalling between daughter cells. InDrosophila pupal sensory organ lineage, Notch regulates the intra-lineage pIIa/pIIb fate decision at cytokinesis. Notch and Delta that localise apically and basally at the pIIa-pIIb interface are expressed at low levels and their residence time at the plasma membrane is in the order of minutes. How Delta can effectively interact with Notch to trigger signalling from a large plasma membrane area remains poorly understood. Here, we report that the signalling interface possesses a unique...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Cell Biology Developmental Biology Source Type: research

Proof of concept for multiple nerve transfers to a single target muscle
This study describes a novel experimental model to investigate the neurophysiological effects of peripheral double nerve transfers. For this purpose, we developed a forelimb model to enable tension-free transfer of one or two donor nerves in the upper extremity. Anatomic dissections were performed to design the double nerve transfer model (n=8). In 62 male Sprague-Dawley rats the ulnar nerve of the antebrachium alone (n=30) or together with the anterior interosseus nerve (n=32) was transferred to reinnervate the long head of the biceps brachii. Before neurotization, the motor branch to the biceps ’ long head was transect...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Neuroscience Source Type: research

HIF1 α stabilization in hypoxia is not oxidant-initiated
Hypoxic adaptation mediated by HIF transcription factors requires mitochondria, which have been implicated in regulating HIF1 α stability in hypoxia by distinct models that involve consuming oxygen or alternatively converting oxygen into the second messenger peroxide. Here, we use a ratiometric, peroxide reporter, HyPer to evaluate the role of peroxide in regulating HIF1α stability. We show that antioxidant enzymes are n either homeostatically induced nor are peroxide levels increased in hypoxia. Additionally, forced expression of diverse antioxidant enzymes, all of which diminish peroxide, had disparate effects on HIF1...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Cell Biology Neuroscience Source Type: research

microRNA-mediated regulation of microRNA machinery controls cell fate decisions
microRNAs associate with Argonaute proteins, forming the microRNA-induced silencing complex (miRISC), to repress target gene expression post-transcriptionally. Although microRNAs are critical regulators in mammalian cell differentiation, our understanding of how microRNA machinery, such as the miRISC, are regulated during development is still limited. We previously showed that repressing the production of one Argonaute protein, Ago2, by Trim71 is important for mouse embryonic stem cells (mESC) self-renewal (Liu et al., 2021). Here we show that among the four Argonaute proteins in mammals, Ago2 is the major developmentally ...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Cell Biology Chromosomes and Gene Expression Source Type: research

Principles of mRNA targeting via the Arabidopsis m < sup > 6 < /sup > A-binding protein ECT2
Specific recognition ofN6-methyladenosine (m6A) in mRNA by RNA-binding proteins containing a YT521-B homology (YTH) domain is important in eukaryotic gene regulation. The Arabidopsis YTH-domain protein ECT2 is thought to bind to mRNA at URU(m6A)Y sites, yet RR(m6A)CH is the canonical m6A consensus site in all eukaryotes and ECT2 functions require m6A binding activity. Here, we apply iCLIP (individual-nucleotide resolution cross-linking and immunoprecipitation) and HyperTRIBE (targets of RNA-binding proteins identified by editing) to define high-quality target sets of ECT2, and analyze the patterns of enriched sequence moti...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Genetics and Genomics Plant Biology Source Type: research

Members of the ELMOD protein family specify formation of distinct aperture domains on the < i > Arabidopsis < /i > pollen surface
Pollen apertures, the characteristic gaps in pollen wall exine, have emerged as a model for studying the formation of distinct plasma membrane domains. In each species, aperture number, position, and morphology are typically fixed; across species they vary widely. During pollen development, certain plasma membrane domains attract specific proteins and lipids and become protected from exine deposition, developing into apertures. However, how these aperture domains are selected is unknown. Here, we demonstrate that patterns of aperture domains inArabidopsis are controlled by the members of the ancient ELMOD protein family, w...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Cell Biology Plant Biology Source Type: research

Mutational analysis to explore long-range allosteric couplings involved in a pentameric channel receptor pre-activation and activation
Pentameric ligand-gated ion channels (pLGICs) mediate chemical signaling through a succession of allosteric transitions that are yet not completely understood as intermediate states remain poorly characterized by structural approaches. In a previous study on the prototypic bacterial proton-gated channel GLIC, we generated several fluorescent sensors of the protein conformation that report a fast transition to a pre-active state, which precedes the slower process of activation with pore opening. Here, we explored the phenotype of a series of allosteric mutations, using paralleled steady-state fluorescence and electrophysiol...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Neuroscience Structural Biology and Molecular Biophysics Source Type: research

A MET-PTPRK kinase-phosphatase rheostat controls ZNRF3 and Wnt signalling
Zinc and ring finger 3 (ZNRF3) is a transmembrane E3 ubiquitin ligase that targets Wnt receptors for ubiquitination and lysosomal degradation. Previously we showed that dephosphorylation of an endocytic tyrosine motif (4Y motif) in ZNRF3 by protein tyrosine phosphatase receptor-type kappa (PTPRK) promotes ZNRF3 internalization and Wnt receptor degradation (Chang et al. 2020). However, a responsible protein tyrosine kinase(s) (PTK) phosphorylating the 4Y motif remained elusive. Here we identify the proto-oncogene MET (mesenchymal-epithelial transition factor) as a 4Y kinase. MET binds to ZNRF3 and induces 4Y phosphorylation...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Cell Biology Source Type: research

The YTHDF proteins ECT2 and ECT3 bind largely overlapping target sets and influence target mRNA abundance, not alternative polyadenylation
Gene regulation viaN6-methyladenosine (m6A) in mRNA involves RNA-binding proteins that recognize m6A via a YT521-B homology (YTH) domain. The plant YTH domain proteins ECT2 and ECT3 act genetically redundantly in stimulating cell proliferation during organogenesis, but several fundamental questions regarding their mode of action remain unclear. Here, we use HyperTRIBE (targets of RNA-binding proteins identified by editing) to show that most ECT2 and ECT3 targets overlap, with only few examples of preferential targeting by either of the two proteins. HyperTRIBE in different mutant backgrounds also provides direct views of r...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Genetics and Genomics Plant Biology Source Type: research

Structure of mycobacterial CIII < sub > 2 < /sub > CIV < sub > 2 < /sub > respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203)
The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than fifty years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIII2CIV2). In mycobacterial electron transport chains, CIII2CIV2 replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidore...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Adaptation and compensation in a bacterial gene regulatory network evolving under antibiotic selection
In this study, we discover that the early evolutionary response ofEscherichia coli to the antibiotic trimethoprim involves derepression of PhoPQ signaling, an Mg2+-sensitive two-component system, by inactivation of the MgrB feedback-regulatory protein. We report that derepression of PhoPQ confers trimethoprim-tolerance toE. coli by hitherto unrecognized transcriptional upregulation of dihydrofolate reductase (DHFR), target of trimethoprim. As a result, mutations inmgrB precede and facilitate the evolution of drug resistance. Using laboratory evolution, genome sequencing, and mutation re-construction, we show that populatio...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Genetics and Genomics Microbiology and Infectious Disease Source Type: research

Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion
Pancreatic cancer has a high mortality rate due to metastasis. Whereas KRAS is mutated in most pancreatic cancer patients, controlling KRAS or its downstream effectors has not been succeeded clinically. ARL4C is a small G protein whose expression is induced by the Wnt and EGF-RAS pathways. In the present study, we found that ARL4C is frequently overexpressed in pancreatic cancer patients and showed that its localization to invasive pseudopods is required for cancer cell invasion. IQGAP1 was identified as a novel interacting protein for ARL4C. ARL4C recruited IQGAP1 and its downstream effector, MMP14, to invasive pseudopods...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Cancer Biology Cell Biology Source Type: research

Adult stem cells and niche cells segregate gradually from common precursors that build the adult Drosophila ovary during pupal development
Production of proliferative Follicle Cells (FCs) and quiescent Escort Cells (ECs) by Follicle Stem Cells (FSCs) in adult Drosophila ovaries is regulated by niche signals from anterior (Cap Cells, ECs) and posterior (polar FCs) sources. Here we show that ECs, FSCs and FCs develop from common pupal precursors, with different fates acquired by progressive separation of cells along the AP axis and a graded decline in anterior cell proliferation. ECs, FSCs and most FCs derive from Intermingled Cell (IC) precursors interspersed with germline cells. Precursors also accumulate posterior to ICs before engulfing a naked germline cys...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Developmental Biology Stem Cells and Regenerative Medicine Source Type: research

First-principles model of optimal translation factors stoichiometry
Enzymatic pathways have evolved uniquely preferred protein expression stoichiometry in living cells, but our ability to predict the optimal abundances from basic properties remains underdeveloped. Here we report a biophysical, first-principles model of growth optimization for core mRNA translation, a multi-enzyme system that involves proteins with a broadly conserved stoichiometry spanning two orders of magnitude. We show that predictions from maximization of ribosome usage in a parsimonious flux model constrained by proteome allocation agree with the conserved ratios of translation factors. The analytical solutions, witho...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Computational and Systems Biology Physics of Living Systems Source Type: research