Biology subjects

Jackson, C. L.

Publications and source records attributed to Jackson, C. L..

6 recordsLinked to original sources

bioRxiv2025

Ancient Protein Resurrection of an ancestral Arf GTPase that regulates membrane trafficking uncovers dual cellular localization and unanticipated properties of modern Arf1 proteins.

The emergence of eukaryotes from their prokaryotic ancestors (eukaryogenesis) marked a fundamental shift in cellular organisation, with the appearance of intracellular compartments including the nucleus, the Golgi apparatus and endosomes. These organelles are part of the endomembrane system of eukaryotic cells, which mediates many processes, including secretion of proteins to the exterior of the cell, uptake of material by endocytosis, and compartmentalized degradation of cellular components. The period of eukaryogenesis after the merger of prokaryotic lineages but preceding the last eukaryotic common ancestor, is inferred to have involved a progressive increase in cellular complexity through expansion of organelle-specific protein machineries. However, the steps and stages of organelle emergence during this period are poorly understood as no extant organisms exist from this period, precluding the use of comparative genomics to determine the properties of ancestral proteins present. Membrane trafficking pathways linking organelles are regulated by Arf family GTPases, including Arf1 and Arf6, both present in the last eukaryotic common ancestor. Here we use ancestral sequence reconstruction and molecular cell biological characterization to explore the properties of the ancestor of the Arf1 and Arf6 GTPases. Arf1 has a major function at the Golgi apparatus in regulation of the secretory pathway, whereas Arf6 regulates endocytic pathways at the plasma membrane and endosomes. Our results indicate that the ancestral Arf1/6 protein localizes to both the Golgi and the plasma membrane. We find that localization to the plasma membrane is due to a C-terminal polybasic motif that unexpectedly is also found in a number of modern Arf1 proteins from a wide diversity of eukaryotes. Our data suggest that the ancestral Arf protein acted at both internal compartments and the cell periphery, a feature preserved in a number of modern Arf1 proteins.

evolutionary biology↗

bioRxiv2025

Lipid transfer by ORP3 is required for the regulation of PI4P and PI(4,5)P2 at the plasma membrane in mitosis

During mitosis, cellular contents including the genetic material and membrane-bound organelles must be faithfully distributed between the two daughter cells. Regulation of PI(4,5)P2 levels at the plasma membrane is essential for mitotic progression, including anchoring of the mitotic spindle, recruitment of the actomyosin cytoskeleton at the cleavage furrow, and abscission. Here, we demonstrate that the ORP3 lipid transfer protein, which transfers PI4P from the plasma membrane to the endoplasmic reticulum (ER) at ER-plasma membrane contacts, plays a crucial role in the regulation of PI4P and PI(4,5)P2 levels at the plasma membrane in mitosis. We show that defects in ORP3 function alter PI4P and PI(4,5)P2 distributions, distribution of the actin cytoskeleton at the plasma membrane, mitotic spindle geometry, chromosome segregation, abscission, and lead to the accumulation of multinucleated cells. The function of ORP3 in mitosis is dependent on its ER-partner VAPA and phosphorylation of the ORP3 VAPA-binding motif strongly recruits ORP3 to the ER, priming it for PI4P transfer from the plasma membrane to the ER. Finally ORP3 is required to prevent PI4P accumulation at the cytoplasmic bridge as a result of PI(4,5)P2 hydrolysis for abscission and successful completion of cell division. Altogether, ORP3 plays a key role in PI4P and PI(4,5)P2 regulation during mitosis. Impairment of ORP3 function results in multiple cell division phenotypes, leading to genetic instability and aneuploidy.

cell biology↗

bioRxiv2024

Arf family GTPases are present in Asgard archaea

The emergence of eukaryotes from their prokaryotic ancestors is one of the most fundamental evolutionary events in the history of life. Little is robustly known about how eukaryogenesis occurred, but a major breakthrough came with the identification of the Asgardarchaeota, the closest prokaryotic lineage to eukaryotes yet discovered. Endomembrane organelles, and the capacity to transport material between them, are major hallmarks of eukaryotic cells. The Arf family GTPases are crucial regulators of organelle dynamics in eukaryotes, functioning in vesicle budding, membrane tethering and membrane-cytoskeleton interactions. Although an expanded GTPase complement has been reported in the Asgardarchaeota, the specific origins of the Arf family remain elusive. Here we report a new group of prokaryotic GTPases, the ArfRs. Widely present in Asgardarchaeota and almost exclusive to them, it is the clade from which all eukaryotic Arf family proteins are derived. Heterologous expression of representative Asgardarchaeota ArfR proteins in the model eukaryote Saccharomyces cerevisiae and X-ray crystallographic studies demonstrate that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results show that Arf family GTPases are present in Asgardarchaeota, and strongly suggest that they originated in the archaeal contributor to eukaryogenesis, providing support for nascent endomembrane system capacity evolving early in eukaryogenesis.

evolutionary biology↗

bioRxiv2021

Immunohistochemical assays for bladder cancer molecular subtyping: Optimizing parsimony and performance using Lund taxonomy

Transcriptomic and proteomic profiling reliably classifies bladder cancers into luminal and basal molecular subtypes. Based on their prognostic and predictive associations, these subtypes may improve clinical management of bladder cancers. However, the complexity of published subtyping algorithms has limited their translation into practice. Here we optimize and validate compact subtyping algorithms based on the Lund taxonomy. We reanalyzed immunohistochemistry (IHC) expression data of muscle-invasive bladder cancer samples from Lund 2017 (n=193) and 2012 (n=76) cohorts. We characterized and quantified IHC expression patterns, and determined the simplest, most accurate decision tree models to identify subtypes. We tested the utility of a previously published algorithm using routine antibody assays commonly available in surgical pathology laboratories (GATA3, KRT5 and p16) to identify basal/luminal subtypes and to distinguish between luminal subtypes, Urothelial-Like (Uro) and Genomically Unstable (GU). We determined the dominant decision tree classifiers using four-fold cross-validation with separate uniformly distributed train (75%) and validation (25%) sets. Using the three-antibody algorithm resulted in 86-95% accuracy across training and validation sets for identifying basal/luminal subtypes, and 67-86% accuracy for basal/Uro/GU subtypes. Although antibody assays for KRT14 and RB1 are not routinely used in pathology practice, these features achieved the simplest and most accurate models to identify basal/luminal and Uro/GU/basal subtypes, achieving 93-96% and 85-86% accuracies, respectively. When translated to a more complex model using eight antibody assays, accuracy was comparable to simplified models, with 86% (train) and 82% (validation). We conclude that a simple immunohistochemical classifier can accurately identify luminal (Uro, GU) and basal subtypes and pave the way for clinical implementation.

pathology↗

bioRxiv2020

A novel isoform of ACE2 is expressed in human nasal and bronchial respiratory epithelia and is upregulated in response to RNA respiratory virus infection

Angiotensin-converting enzyme 2 (ACE2) is the main entry point in the airways for SARS-CoV-2. ACE2 binding to SARS-CoV-2 protein Spike triggers viral fusion with the cell membrane, resulting in viral RNA genome delivery into the host. Despite ACE2s critical role in SARS-CoV-2 infection, an understanding of ACE2 expression, including in response to viral infection, remains unclear. Until now ACE2 was thought to encode five transcripts and one 805 amino acid protein. Here we identify a novel short isoform of ACE2. Short ACE2 is expressed in the airway epithelium, the main site of SARS-CoV-2 infection; it is substantially upregulated in response to interferon stimulation and RV infection, but not in response to SARS-CoV-2 infection, and it shows differential regulation in asthma patients. This short isoform lacks SARS-CoV-2 spike glycoprotein high-affinity binding sites and altogether, our data are consistent with a model where short ACE2 may influence host susceptibility to SARS-CoV-2 infection.

molecular biology↗

bioRxiv2018

A giant amphipathic helix from a perilipin that is adapted for coating lipid droplets

How proteins are targeted to lipid droplets (LDs) and distinguish the LD surface from the surfaces of other organelles is poorly understood, but many contain predicted amphipathic helices (AHs) that are involved in targeting. We have focused on human perilipin 4 (Plin4), which contains an AH that is exceptional in terms of length and repetitiveness. Using model cellular systems, we show that AH length, hydrophobicity, and charge are important for AH targeting to LDs and that these properties can compensate for one another, albeit at a loss of targeting specificity. Using synthetic lipids, we show that purified Plin4 AH binds poorly to lipid bilayers but strongly interacts with pure triglycerides, acting as a coat and forming small oil droplets. Because Plin4 overexpression alleviates LD instability under conditions where their coverage by phospholipids is limiting, we propose that the Plin4 AH replaces the LD lipid monolayer, for example during LD growth.

cell biology↗