Biology subjects

Hughes, A. L.

Publications and source records attributed to Hughes, A. L..

15 recordsLinked to original sources

bioRxiv2026

Mitochondrial-derived compartments buffer outer membrane protein load during acute mitochondrial adaptation

Cells undergoing metabolic transitions rapidly remodel mitochondria through coordinated expansion and reorganization of the mitochondrial proteome. How the outer mitochondrial membrane (OMM) accommodates acute increases in newly synthesized proteins before organelle adaptation is complete remains poorly understood. Here we show that mitochondrial-derived compartments (MDCs), multilamellar domains that form from the OMM and selectively sequester OMM-associated cargo, arise during metabolic perturbations associated with acute mitochondrial biogenesis, including glucose restriction, carbon-source switching, and salt stress. In these situations, MDC formation requires the energy-sensing kinase Snf1 and derepression of the transcriptional repressor Mig1, linking MDC induction to transcriptional programs that increase mitochondrial protein expression. Activation of mitochondrial biogenesis in the absence of metabolic changes is sufficient to trigger MDCs, whereas disruption of mitochondrial protein targeting and import prevents MDC formation and causes mislocalization of outer membrane cargos. Together, these findings, combined with previous observations that MDCs are induced by hydrophobic protein overexpression, mistargeting, and metabolic perturbations, support an emerging model in which MDCs function as adaptive outer-membrane remodeling domains that buffer outer membrane protein load during mitochondrial adaptation.

cell biology↗

bioRxiv2026

Vacuole pH loss triggers ESCRT-dependent plasma membrane remodeling to prevent amino acid toxicity

Loss of lysosomal or vacuolar acidity is a hallmark of aging, metabolic dysfunction, and cellular stress, yet how cells adapt to this condition remains poorly understood. In budding yeast, where the vacuole serves as a major reservoir for intracellular amino acids, impaired vacuolar acidification disrupts amino acid homeostasis. Here we performed a genome-wide screen in budding yeast to identify pathways required for survival during vacuole pH stress. We found that endocytic trafficking and ESCRT/MVB components become essential when vacuolar acidification is disrupted. Vacuole deacidification triggered ESCRT-dependent rerouting and degradation of plasma membrane amino acid transporters, thereby limiting nutrient influx. Blocking this response stabilized transporters at the cell surface and caused synthetic lethality under vacuole stress. This growth defect was suppressed by lowering amino acid availability or reducing transporter expression, whereas amino acid supplementation restored toxicity. Nitrogen starvation prevented transporter internalization, indicating that nutrient status gates this adaptive response. Together, these findings reveal a vacuole-plasma membrane communication pathway that protects cells from amino acid toxicity by matching nutrient influx to vacuolar function.

cell biology↗

bioRxiv2026

Proteolytic remodeling by Yme1 enables mitochondrial-derived compartment formation

Mitochondrial-derived compartments (MDCs) are remodeling domains that form from the outer mitochondrial membrane during metabolic and proteotoxic stress and selectively sequester hydrophobic membrane proteins. Although MDC formation depends on mitochondrial lipid composition and occurs at organelle contact sites, the molecular mechanisms that permit their biogenesis remain poorly defined. Here we identify the conserved inner mitochondrial membrane i-AAA protease Yme1 as a critical regulator of MDC formation. Loss of Yme1 blocks MDC biogenesis in response to multiple stressors, and this requirement depends on its proteolytic activity rather than secondary defects in mitochondrial morphology. Quantitative mitochondrial proteomics under MDC-inducing conditions revealed Yme1-dependent remodeling of lipid transfer proteins of the Ups family and components of the MICOS complex. Disruption of either pathway partially restores MDC formation in yme1{Delta} cells, while combined perturbation substantially bypasses the requirement for Yme1. Finally, Yme1 overexpression drives MDC formation in the absence of stress, although this activity remains constrained by metabolic conditions. Together, these findings support a model in which Yme1-dependent proteolysis relieves lipid- and MICOS-dependent constraints to permit MDC formation.

cell biology↗

bioRxiv2025

SET1/MLL complexes control transcription independently of H3K4me3

Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein complexes, but discovering how these essential enzymes shape H3K4me3 has been extremely challenging due to their multiplicity. This has also made determining whether SET1/MLL complexes control transcription through H3K4me3, or non-catalytic activities, an impenetrable problem. Here, we overcome these challenges through leveraging genome-engineering and combinatorial SET1/MLL protein depletion, integrated with genomics, proteomics, and live-cell transcription imaging. We uncover a new SET1B complex and reveal that SET1 and MLL1/2 complexes synergise to define H3K4me3 at gene regulatory elements. Unexpectedly, by decoupling SET1/MLL complex occupancy at promoters from H3K4me3, we discover they primarily control transcription independently of H3K4me3 through counteracting promoter-proximal termination and supporting transcription burst size. These discoveries reveal a new H3K4me3-independent logic for SET1/MLL-dependent control of gene transcription.

genomics↗

bioRxiv2025

Alterations in Lipid Saturation Trigger Remodeling of the Outer Mitochondrial Membrane

Lipid saturation is a key determinant of membrane function and organelle health, with changes in saturation triggering adaptive quality control mechanisms to maintain membrane integrity. Among cellular membranes, the mitochondrial outer membrane (OMM) is an important interface for many cellular functions, but how lipid saturation impacts OMM function remains unclear. Here, we show that increased intracellular unsaturated fatty acids (UFAs) remodel the OMM by promoting the formation of multilamellar mitochondrial-derived compartments (MDCs), which sequester proteins and lipids from the OMM. These effects depend on the incorporation of UFAs into membrane phospholipids, suggesting that changes in membrane bilayer composition mediate this process. Furthermore, elevated UFAs impair the assembly of the OMM protein translocase (TOM) complex, with unassembled TOM components captured into MDCs. Collectively, these findings suggest that alterations in phospholipid saturation may destabilize OMM protein complexes and trigger an adaptive response to sequester excess membrane proteins through MDC formation. Significance StatementO_LIMitochondrial-derived compartments are multilamellar structures that sequester protein and lipids of the outer mitochondrial membrane in response to metabolic and membrane perturbations, but it is largely unknown how membrane fluidity influences this pathway. C_LIO_LIIncreased levels of unsaturated phospholipids may disrupt the TOM complex, a large multi-subunit complex on the outer mitochondrial membrane, to promote the formation of mitochondrial-derived compartments, while increased levels of saturated phospholipids inhibits formation of mitochondrial-derived compartments. C_LIO_LIThese findings reveal a link between phospholipid composition and protein stress in driving mitochondrial-derived compartment biogenesis, and thus mitochondrial quality control. C_LI

cell biology↗

bioRxiv2023

Genetic Screen Uncovers a Dual Role for Phospholipids in Mitochondrial-Derived Compartment Biogenesis

Cells utilize multiple mechanisms to maintain mitochondrial homeostasis in response to stress. We recently identified a cellular structure, called the mitochondria-derived compartment (MDC), that is generated from mitochondria in response to amino acid overabundance. MDCs selectively sequester proteins from mitochondria for subsequent degradation, and loss of MDCs sensitizes cells to amino acid stress. Here, we conducted a microscopy-based screen in budding yeast to identify factors that regulate MDC formation. We found that levels of two mitochondrial phospholipids, cardiolipin (CL) and phosphatidylethanolamine (PE), regulate MDC biogenesis in opposing directions. CL depletion impairs MDC biogenesis, whereas PE reduction leads to constitutive MDC formation. Additionally, in response to MDC-inducing agents, cellular and mitochondrial PE declines in an amino acid-dependent manner. Overexpressing mitochondrial PE synthesis pathway components suppresses MDC biogenesis during amino acid stress. Altogether, our data indicate a requirement for CL in MDC biogenesis, and suggest that PE depletion may serve as a regulatory signal for MDC formation downstream of MDC-inducing metabolic stress. SUMMARYXiao et al. identify distinct roles for the phospholipids cardiolipin and phosphatidylethanolamine in mitochondria-derived compartment (MDC) biogenesis. They show that cardiolipin is required for MDC formation, whereas a decline in phosphatidylethanolamine in response to amino acid stress triggers MDC biogenesis.

cell biology↗

bioRxiv2022

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions

The Sc2.0 project is building a eukaryotic synthetic genome from scratch, incorporating thousands of designer features. A major milestone has been achieved with the assembly of all individual Sc2.0 chromosomes. Here, we describe the consolidation of multiple synthetic chromosomes using endoreduplication intercross to generate a strain with 6.5 synthetic chromosomes. Genome-wide chromosome conformation capture and long-read direct RNA sequencing were performed on this strain to evaluate the effects of designer modifications, such as loxPsym site insertion, tRNA relocation, and intron deletion, on 3D chromosome organization and transcript isoform profiles. To precisely map "bugs", we developed a method, CRISPR Directed Biallelic URA3-assisted Genome Scan, or "CRISPR D-BUGS", exploiting directed mitotic recombination in heterozygous diploids. Using this method, we first fine-mapped a synII defect resulting from two loxPsym sites in the 3 UTR of SHM1. This approach was also used to map a combinatorial bug associated with synIII and synX, revealing a highly unexpected genetic interaction that links transcriptional regulation, inositol metabolism and tRNASerCGA abundance. "Starvation" for tRNASerCGA leads to insufficient levels of the key positive inositol biosynthesis regulator, Swi3, which contains tandem UCG codons. Finally, to expedite consolidation, we employed a new method, chromosome swapping, to incorporate the largest chromosome (synIV), thereby consolidating more than half of the Sc2.0 genome in a single strain.

genomics↗

bioRxiv2022

A CpG island-encoded mechanism protects genes from premature transcription termination

Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. Counterintuitively, this effect is independent of SET1 complex histone modifying activity, and instead relies on the capacity of these complexes to interact with the RNA Polymerase II-binding protein, WDR82. Unexpectedly, we discover that SET1 complexes sustain gene transcription by counteracting the activity of the ZC3H4/WDR82 protein complex, which we show can pervasively terminate both genic and extragenic transcription. Therefore, we discover a new gene regulatory mechanism whereby CpG island elements nucleate a protein complex that protects genic transcription from premature termination, effectively distinguishing genic from non-genic transcription to enable gene expression.

molecular biology↗

bioRxiv2020

Amino Acids Promote Mitochondrial-Derived Compartment Formation in Mammalian Cells

We recently identified a new cellular structure in yeast, called the Mitochondrial-Derived Compartment (MDC), that forms on mitochondria in response to amino acid excess. While emerging evidence supports an important function for MDCs in protecting cells from metabolic stress, whether this system exists beyond yeast remains unclear. Here, we show that MDCs are conserved in mammals, and like their yeast counterparts, are responsive to the intracellular amino acid content. Specifically, we find that inhibition of protein translation stimulates formation of dynamic, micron-sized compartments that associate with the mitochondrial network. These compartments are enriched for the carrier receptor Tomm70A and other select mitochondrial outer and inner membrane cargo, associate with the ER membrane, and require the conserved GTPase Miro1 for formation. Mammalian MDCs are responsive to changes in amino acid levels during translation inhibition, and are not activated by other common cellular stressors. Thus, MDCs represent an evolutionarily conserved nutrient-responsive mitochondrial remodeling system.

cell biology↗

bioRxiv2020

The Nucleus is a Quality Control Center For Non-Imported Mitochondrial Proteins

Mitochondrial import deficiency causes cellular stress due to the accumulation of non-imported mitochondrial precursor proteins. Despite the burden mis-localized mitochondrial precursors place on cells, our understanding of the systems that dispose of these proteins is incomplete. Here, we catalog the location and steady-state abundance of mitochondrial precursor proteins during mitochondrial impairment in S. cerevisiae. We find that a number of non-imported mitochondrial proteins localize to the nucleus, where they are eliminated by proteasome-based nuclear protein quality control. Recognition of mitochondrial precursors by the nuclear quality control machinery requires the presence of an N-terminal mitochondrial targeting sequence (MTS), and impaired breakdown of precursors leads to their buildup in nuclear-associated foci. These results identify the nucleus as a key destination for the disposal of non-imported mitochondrial precursors.

cell biology↗

bioRxiv2020

The GET Pathway Safeguards Against Non-Imported Mitochondrial Protein Stress

Deficiencies in mitochondrial import cause the toxic accumulation of non-imported mitochondrial precursor proteins. Numerous fates for non-imported mitochondrial precursors have been identified, including proteasomal destruction, deposition into protein aggregates, and mis-targeting to other organelles. Amongst organelles, the endoplasmic reticulum (ER) has emerged as a key destination for non-imported mitochondrial proteins, but how ER-targeting of these proteins is achieved remains unclear. Here, we show that the guided entry of tail-anchored proteins (GET) complex is required for ER-targeting of endogenous mitochondrial multi-transmembrane proteins. Without a functional GET pathway, non-imported mitochondrial proteins destined for the ER are alternatively sequestered into Hsp42-dependent protein foci. The ER targeting of non-imported mitochondrial proteins by the GET complex prevents cellular toxicity and facilitates re-import of mitochondrial proteins from the ER via the recently identified ER-SURF pathway. Overall, this study outlines an important and unconventional role for the GET complex in mitigating stress associated with non-imported mitochondrial proteins.

cell biology↗

bioRxiv2020

Mitochondrial-Derived Compartments Facilitate Cellular Adaptation to Amino Acid Stress

Amino acids are essential building blocks of life. However, increasing evidence suggests that elevated amino acids cause cellular toxicity associated with numerous metabolic disorders. How cells cope with elevated amino acids remains poorly understood. Here, we show that a previously identified cellular structure, the mitochondrial-derived compartment (MDC), is a dynamic, lumen-containing organelle that functions to protect cells from amino acid stress. In response to amino acid elevation, MDCs are generated from mitochondria, where they selectively sequester and remove Tom70, a surface receptor required for import of nutrient carriers of the SLC25 family. MDC formation is regulated by levels of mitochondrial carriers, and its activation by amino acids occurs simultaneously with removal of plasma membrane-localized transporters via the multi-vesicular body (MVB) pathway. Combined loss of MDC and MVB formation renders cells sensitive to elevated amino acids, suggesting these pathways operate as a coordinated network to protect cells from amino acid toxicity.

cell biology↗

bioRxiv2020

ER-Mitochondria Contacts Promote Mitochondrial-Derived Compartment Biogenesis

Mitochondria are dynamic organelles with essential roles in signaling and metabolism. We recently identified a new cellular structure called the mitochondrial-derived compartment (MDC) that is generated from mitochondria in response to amino acid elevation. MDCs protect cells from amino acid toxicity, but how cells form MDCs is unclear. Here, we show that MDCs are micron-sized, lumen-containing organelles that form at sites of contact between the ER and mitochondria. Upon formation, MDCs stably persist at ER-mitochondria contacts for extended periods of time. MDC formation requires the ER-mitochondria encounter structure (ERMES) and GTP hydrolysis by the conserved GTPase Gem1. Unexpectedly, MDC formation is not linked to the role of ERMES/Gem1 in the maintenance of mitochondrial phospholipid homeostasis. Our results identify an important role for ER-mitochondria contacts in the biogenesis of MDCs. Abbreviations used in this paper: ERMES, ER-mitochondria encounter structure; IMM, inner mitochondrial membrane; MDC, mitochondrial-derived compartment; OMM, outer mitochondrial membrane. SummaryEnglish et al. use super-resolution imaging to show that mitochondrial-derived compartments are lumen-containing organelles that form at sites of contact between the ER and mitochondria. Mitochondrial-derived compartment biogenesis requires a noncanonical function of the ERMES complex and the conserved GTPase Gem1.

cell biology↗

bioRxiv2018

Chaos Game Representation: An Alignment-Free Technique for Exploring Evolutionary Relationships of Protein Sequences

Chaos Game Representation (CGR) is an iterative mapping technique, which shows patterns in amino acids or nucleotide sequences. Here we present a method for using CGR to explore evolutionary relationships of protein sequences based on amino acid properties and illustrate the approach with complete sets of protein translations from viral genomes. In an analysis of complete polyprotein sequences from the viral family Flaviviridae, the CGR method was able to cluster members of major viral groups together, but relations within groups were not well resolved in comparison to an alignment-based phylogeny. We applied the method to members of five different families of ssRNA positive-strand viruses, and each family formed a distinct cluster. We also present a method of testing the reliability of clustering in CGR-based trees, which involves the use of multiple random starting points for the CGR process.

evolutionary biology↗

bioRxiv2016

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.

The yeast Chd1 protein acts to position nucleosomes across genomes. Here we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state the DNA binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavourable alignment of C-terminal DNA binding region in solution contributes to an auto-inhibited state.

molecular biology↗