Biology subjects

Jones, R. A.

Publications and source records attributed to Jones, R. A..

10 recordsLinked to original sources

bioRxiv2026

Intracellular screening of nanobodies reveals an intrabody that inhibits ITCH E3 ubiquitin ligase

Nanobodies are a class of small, monomeric camelid antibody fragments that can bind target antigens with high affinity and specificity. Their small size, structural simplicity, and limited reliance on disulfide bonding makes them attractive for intracellular expression for labeling and perturbing cellular processes in live cells. However, screening campaigns carried out exclusively in vitro often yield antigen binders that fail to perform well in live cells due to low expression, misfolding, or mistargeting. We demonstrate that traditional in vitro screening of a nanobody library combined with an intracellular bioluminescence resonant energy transfer (BRET) proximity sensor approach for sequence down-selection can yield strong in vitro binders that also perform well as intrabodies, in this case capable of binding to, and inhibiting the enzymatic activity of, ITCH E3 ubiquitin ligase in human cells. This strategy allows a more direct and scalable path toward intrabody discovery.

cell biology↗

bioRxiv2025

Dynamic and atypical E-cadherin-based attachments mediate melanoblast migration through confined epithelial spaces

Epithelial tissues are populated with accessory cells such as immune cells, sensory cells, and pigment-producing melanocytes, which must migrate through and intercalate between tightly adherent epithelial cells. Although much is known about how cells migrate through interstitial spaces consisting of predominantly of collagen-rich ECM and mesenchyme, how cells migrate through confined epithelial spaces without impairing barrier function is far less understood. Here, using live imaging of the mouse epidermis, we captured the migration of embryonic melanocytes (melanoblasts) while simultaneously visualizing the basement membrane or epithelial surfaces. We show that melanoblasts migrate through both basal and suprabasal layers of the epidermis and hair follicles where they use keratinocyte surfaces, as well as the basement membrane, as substrates for migration. We show that melanoblasts form atypical and dynamic E-cadherin based attachments to surrounding keratinocytes that largely lack the cytoplasmic catenins known to anchor E-cadherin to the actin cytoskeleton. We show E-cadherin is needed in both melanoblasts and keratinocytes to stabilize migratory protrusions, and that depleting E-cadherin in melanoblasts results in reduced motility and ventral depigmentation in adult mice. These findings illustrate how migratory cells co-opt the cell-cell adhesion machinery connecting adjacent epithelial cells to invade between and migrate through them without interrupting the skin barrier.

cell biology↗

bioRxiv2024

Human DNA replication initiation sites are specified epigenetically by oxidation of 5-methyl-deoxycytidine

DNA replication initiates at tens of thousands of sites on the human genome during each S phase. However, no consensus DNA sequence has been found that specifies the locations of these replication origins. Here, we investigate modifications of human genomic DNA by density equilibrium centrifugation and DNA sequencing. We identified short discrete sites with increased density during quiescence and G1 phase that overlap with DNA replication origins before their activation in S phase. The increased density is due to the oxidation of 5-methyl-deoxycytidines by TET enzymes at GC-rich domains. Reversible inhibition of de novo methylation and of subsequent oxidation of deoxycytidines results in a reversible inhibition of DNA replication and of cell proliferation. Our findings suggest a mechanism for the epigenetic specification and semiconservative inheritance of DNA replication origin sites in human cells that also provides a stable integral DNA replication licence to support once-per-cell cycle control of origin activation.

biochemistry↗

bioRxiv2024

Zebrafish reveal new roles for Fam83f in hatching and the DNA damage-mediated autophagic response

The FAM83 (Family with sequence similarity 83) family is highly conserved in vertebrates, but little is known of the functions of these proteins beyond their association with oncogenesis. Of the family, FAM83F is of particular interest because it is the only membrane-targeted FAM83 protein. When over-expressed, FAM83F activates the canonical Wnt signalling pathway and binds to and stabilizes p53; it therefore interacts with two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development, and here we report the generation of fam83f knock-out (KO) zebrafish, which we have used to study the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the hatching gland of developing zebrafish embryos, and that fam83f KO embryos hatch earlier than their wild-type (WT) counterparts, despite developing at a comparable rate. We also demonstrate that fam83f KO embryos are more sensitive to ionizing radiation than WT embryos--an unexpected finding, bearing in mind the previously-reported ability of FAM83F to stabilize p53. Transcriptomic analysis shows that loss of fam83f leads to downregulation of phosphatidylinositol-3-phosphate (PI(3)P) binding proteins and impairment of cellular degradation pathways, particularly autophagy, a crucial component of the DNA damage response. Finally, we show that Fam83f protein is itself targeted to the lysosome when over-expressed in HEK293T cells, and that this localization is dependent upon a C terminal signal sequence. The zebrafish lines we have generated suggest that Fam83f plays an important role in autophagic/lysosomal processes, resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo.

developmental biology↗

bioRxiv2023

A Window into Mammalian Basement Membrane Development: Insights from the mTurq2-Col4a1 Mouse Model

Basement membranes (BMs) are specialized sheets of extracellular matrix that underlie epithelial and endothelial tissues. BMs regulate traffic of cells and molecules between compartments, and participate in signaling, cell migration and organogenesis. The dynamics of mammalian BMs, however, are poorly understood, largely due to a lack of models in which core BM components are endogenously labelled. Here, we describe the mTurquoise2-Col4a1 mouse, in which we fluorescently tag collagen IV, the main component of BMs. Using an innovative Planar-Sagittal live imaging technique to visualize the BM of developing skin, we directly observe BM deformation during hair follicle budding and basal progenitor cell divisions. The BMs inherent pliability enables dividing cells to remain attached to and deform the BM, rather than lose adhesion as generally thought. Using FRAP, we show BM collagen IV is extremely stable, even during periods of rapid epidermal growth. These findings demonstrate the utility of the mTurq2-Col4a1 mouse to shed new light on mammalian BM developmental dynamics.

cell biology↗

bioRxiv2023

Automated staging of zebrafish embryos with KimmelNet

The zebrafish (Danio rerio), is an important biomedical model organism used in many disciplines. The phenomenon of developmental delay in zebrafish embryos has been widely reported as part of a mutant or treatment-induced phenotype. However, the detection and quantification of these delays is often achieved through manual observation with reference to staging guides, which is both time-consuming and subjective. We recently reported a machine learning-based classifier, capable of quantifying the developmental delay between two populations of zebrafish embryos. Here, we build on that work by introducing a deep learning-based model (KimmelNet) that has been trained to predict the age (hours post fertilisation) of populations of zebrafish embryos. We show that when KimmelNet is tested on 2D brightfield images of zebrafish embryos, the predictions generated agree closely with those expected from established approaches to staging. Random sampling of the test data demonstrate that KimmelNet can be used to detect developmental delay between two populations with high confidence based on as few as 100 images of each population. Finally, we show that KimmelNet generalises to previously unseen data, with limited transfer learning improving this performance significantly. With the ability to analyse tens of thousands of standard brightfield microscopy images on a timescale of minutes, we envisage that KimmelNet will be a valuable resource for the developmental biology community. Furthermore, the approach we have used could easily be adapted to generate models for other organisms.

developmental biology↗

bioRxiv2020

Different tertiary interactions create the same important 3-D features in a divergent flavivirus xrRNA

During infection by a flavivirus (FV), cells accumulate noncoding subgenomic flavivirus RNAs (sfRNAs) that interfere with several antiviral pathways. These sfRNAs are formed by structured RNA elements in the 3' untranslated region (UTR) of the viral genomic RNA, which block the progression of host cell exoribonucleases that have targeted the viral RNA for destruction. Previous work on these exoribonuclease-resistant RNAs (xrRNAs) from mosquito-borne FVs revealed a specific 3-dimensional fold with a unique topology in which a ring-like structure protectively encircles the 5' end of the xrRNA. Conserved nucleotides make specific tertiary interactions that support this fold. Examination of more divergent FVs reveals differences in their 3' UTR sequences, raising the question of whether they contain xrRNAs and if so, how they fold. To answer this, we demonstrated the presence of an authentic xrRNA in the 3' UTR of the Tamana Bat Virus (TABV) and solved its structure by x-ray crystallography. The structure reveals conserved features from previously characterized xrRNAs, but in the TABV version these features are created through a novel set of tertiary interactions not previously seen in xrRNAs. This includes two important A-C interactions, four distinct backbone kinks, several ordered Mg2+ ions, and a C+-G-C base triple. The discovery that the same overall architecture can be achieved by very different sequences and interactions in distantly related flaviviruses provides insight into the diversity of this type of RNA and will inform searches for undiscovered xrRNAs in viruses and beyond.

biochemistry↗

bioRxiv2020

A new subclass of exoribonuclease resistant RNA found in multiple Flaviviridae genera

Viruses have developed innovative strategies to exploit the cellular machinery and overcome the host antiviral defenses, often using specifically structured RNA elements. Examples are found in flaviviruses; during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5 to 3 exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease resistant RNA structure (xrRNA) located in the viral genomes 3untranslated region (UTR). Although known to exist in several Flaviviridae genera the full distribution and diversity of xRNAs in this virus family was unknown. Using the recent high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNA in the Pegivirus, Pestivirus, and Hepacivirus genera. We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Our findings thus require adjustments of previous xrRNA classification schemes and expand on the previously known distribution of the xrRNA in Flaviviridae, indicating their widespread distribution and illustrating their importance. IMPORTANCEThe Flaviviridae comprise one of the largest families of positive sense single stranded (+ssRNA) and it is divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika Virus, Dengue Virus, and Powassan Virus. In these, a part of the viruss RNA twists up into a very special three-dimensional shape called an xrRNA that blocks the ability of the cell to "chew up" the viral RNA. Hence, part of the virus RNA remains intact, and this protected part is important for viral infection. This was known to occur in Flaviviruses but whether it existed in the other members of the family was not known. In this study, we not only identified a new subclass of xrRNA found in Flavivirus but also in the remaining three genera. The fact that this process of viral RNA maturation exists throughout the entire Flaviviridae family makes it clear that this is an important but underappreciated part of the infection strategy of these diverse human pathogens.

microbiology↗

bioRxiv2020

FAM83F regulates canonical Wnt signalling through an interaction with CK1α

The function of the FAM83F protein, like the functions of many members of the FAM83 family, is poorly understood. Here we show that injection of Fam83f mRNA into Xenopus embryos causes axis duplication, a phenotype indicative of enhanced Wnt signalling. Consistent with this, overexpression of FAM83F activates Wnt signalling, whilst ablation of FAM83F from human colorectal cancer (CRC) cells attenuates it. We demonstrate that FAM83F is farnesylated and interacts and co-localises with CK1 at the plasma membrane. This interaction with CK1 is essential for FAM83F to activate Wnt signalling, and FAM83F mutants that do not interact with CK1 fail to induce axis duplication in Xenopus embryos and to activate Wnt signalling in cells. FAM83F acts upstream of the {beta}-catenin destruction complex, because the attenuation of Wnt signalling caused by loss of FAM83F can be rescued by GSK-3 inhibition. Introduction of a farnesyl-deficient mutant mis-localises the FAM83F-CK1 complex to the nucleus and significantly attenuates Wnt signalling, indicating that FAM83F exerts its effects on Wnt signalling at the plasma membrane.

cell biology↗

bioRxiv2019

The type VII secretion system protects Staphylococcus aureus against antimicrobial host fatty acids

The Staphylococcus aureus type VII secretion system (T7SS) exports several proteins that are pivotal for bacterial virulence. The mechanisms underlying T7SS-mediated staphylococcal survival during infection nevertheless remain unclear. Here we show that the absence of EsxC, a small secreted effector implicated in bacterial persistence, results in cell membrane defects in S. aureus. Interestingly, isogenic mutants lacking EsxC, other T7SS effectors EsxA and EsxB, or the membrane-bound ATPase EssC, are more sensitive to killing by the host-derived antimicrobial fatty acid, linoleic acid (LA), compared to the wild-type (WT). LA induces more cell membrane damage in the T7SS mutants compared to the WT. Although WT and mutant strains did not differ in their ability to bind labelled LA, membrane lipid profiles show that T7SS mutants are less able to incorporate LA into their membrane phospholipids. Furthermore, proteomic analyses of WT and mutant cell fractions reveal that, in addition to compromising membranes, T7SS defects induce oxidative stress and hamper their response to LA challenge. Thus, our findings indicate that T7SS is crucial for S. aureus membrane integrity and homeostasis, which is critical when bacteria encounter antimicrobial fatty acids.

microbiology↗