Biology subjects

Yu, H. H.

Publications and source records attributed to Yu, H. H..

4 recordsLinked to original sources

bioRxiv2025

Single-cell transcriptomic dynamics exposes hidden survival trajectory under antibiotic treatment

Heterogeneity plays a major role in bacterial resistance to antibiotic treatment while the mechanism at single-cell level is largely unknown. Here, we employed a robust integration of bulk and bacterial single-cell RNA-seq (scRNA-seq) to uncover how individual cells of Acinetobacter baumannii reorganise the heterogenous transcriptome in response to antibiotic. Using polymyxin as a representative, bulk RNA-seq showed canonical envelope- and efflux-centred responses but obscured underlying heterogeneity. Single-cell profiling resolved these averages into discrete subpopulations whose abundances shifted with concentration and time. Specifically, in early time an envelope-stress programme predominated survival at the low concentration, whereas an outer-membrane repair/efflux programme dominated survival at the high concentration. These patterns revealed structured and time-resolved heterogeneity, highlighting an ingenious bacterial stress responsive strategy. Through trajectory inference, we further revealed a concentration-dependent bifurcation of cell fates: low-concentration treated cells detoured through a transient stress state and rejoined growth, whereas high-concentration treated survivors diverted into a slow-growing, tolerant branch. Perturbing marker genes from these programmes altered fitness eventually and rapidly increased permeability, depolarisation and reactive-oxygen burden, linking state to survival capability. Collectively, we map a dynamic, concentration-structured landscape of antibiotic responses at the single-cell level, revealing diverse survival trajectories that are obscured in conventional population-averaged analyses. Our developed single-cell based framework revealed tolerant bacterial cells with rewiring of the transcriptional landscape, causing emergence of antibiotic resistance. Importantly, these findings urge precision antimicrobial therapy in patients to minimise emergence of antibiotic resistance.

microbiology↗

bioRxiv2024

Temperature-sensitive cortical condensation modulates mechano-response at Tricellular Junctions

A general mechanism to maintain epithelial integrity during cell movements is to couple adhesion strength with mechanical force. Mechanosensitive proteins are recruited to adhesion sites to reinforce cell-cell or cell-matrix linkage in response to elevated tension. However, subcellular mechanisms for highly dynamic protein transport into and out of tension-bearing structures remain elusive. Furthermore, it is still unknown whether mechanosensitivity can be modulated by physiological signals in vivo. Here we revealed a direct "edge-to-vertex" route of Canoe/Afadin transport to tricellular junctions under tension, which relies on an obligatory binding partner Mbt/PAK. Without Mbt/PAK, Canoe/Afadin becomes insensitive to cytoskeletal tension and forms "tactoid-shaped" condensates directly at bicellular junctions. Remarkably, a temporary increase in temperature within the physiological range dissolves these condensates, allowing Canoe/Afadin to regain mechanosensitivity and enrichment at tricellular junctions. Functionally, the localization of Mbt/PAK at cell junctions oscillates during synchronous cell division within embryonic mitotic domains, enabling dynamic adjustments of Canoe/Afadin mechanosensitivity to preserve epithelial integrity in rapidly dividing tissues. Collectively, our findings suggest a physiological process in which the state of protein condensation, regulated by biochemical inputs, can supersede mechanical signals to modulate adhesion strength during cell division.

cell biology↗

bioRxiv2019

Single subunit degradation of WIZ, a lenalidomide- and pomalidomide dependent substrate of E3 ubiquitin ligase CRL4CRBN

Immunomodulators (IMiDs) are an effective class of drugs used to treat blood cancers. IMiDs are believed to work by recruiting protein targets containing a {beta}-hairpin motif for ubiquitination by E3 ubiquitin ligase complexes composed of cereblon (CRBN), Cullin-4a (CUL4a), DNA Damage Binding protein-1 (DDB1), and Ring Box-1 (RBX1). The ubiquitinated protein is subsequently degraded by the proteasome. By characterizing the repertoire of proteins that show an increased physical association with CRBN after IMiD treatment, we identified a novel IMiD substrate, Widely Interspaced Zinc Finger Motifs (WIZ). WIZ contains a C2H2 zinc finger domain, like several other substrates that were previously characterized. We demonstrate that IMiDs stabilize physical association of WIZ with CRBN, deplete WIZ steady state protein levels in a way that is dependent on E3 ligase activity, and enhance the rate of its degradation. Notably, proteins that assemble with WIZ are co-recruited to CRBN by IMiDs but are not degraded, illustrating the potential of targeted protein degradation to eliminate individual subunits of a protein complex. These findings suggest that systematic characterization of the full repertoire of proteins that are targeted for degradation by IMiD compounds will be required to better understand their biological effects.\n\nSynopsisProteolysis Targeting Chimeras (PROTACs) can be used to precisely target a subunit of a transcriptional complex for degradation in subpopulations of cells.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC=\"FIGDIR/small/595389_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@186fed8org.highwire.dtl.DTLVardef@1c522f9org.highwire.dtl.DTLVardef@17b19baorg.highwire.dtl.DTLVardef@d626ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2017

DNA unwinding is the primary determinant of CRISPR-Cas9 activity

Bacterial adaptive immunity utilizes RNA-guided surveillance complexes composed of CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR RNAs (crRNAs) to target foreign nucleic acids for destruction. Cas9, a type II CRISPR-Cas effector complex, can be programed with a single guide RNA that base-pairs with the target strand of dsDNA, displacing the non-target strand to create an R-loop, where the HNH and RuvC nuclease domains can cleave opposing strands. Cas9 has been repurposed for a variety of important genome engineering applications. While many structural and biochemical studies have shed light on the mechanism of Cas9 cleavage, a clear unifying model has yet to emerge. Our detailed kinetic characterization of the enzyme reveals that DNA binding is reversible, R-loop formation is rate-limiting, occurring in two steps, one for each of the nuclease domains. Although the HNH nuclease activity is stimulated by Mg2+ with a single measureable Kd, the RuvC activity requires two distinct Mg2+ binding events. The specificity constant for cleavage is determined through an induced-fit mechanism as the product of the equilibrium binding affinity for DNA and the rate of R-loop formation.

biochemistry↗