Biology subjects

Lim, S. L.

Publications and source records attributed to Lim, S. L..

6 recordsLinked to original sources

bioRxiv2026

Resilience and reassembly of redox-structured microbial functional networks after rare holomixis in a meromictic lake

Abstract-shortLand-locked meromictic lakes are characterized by long-term stratification and steep redox gradients that sustain vertically structured microbial communities and tightly coupled biogeochemical processes. Because complete overturns of the lake are rare, the dynamics of microbial reassembly after redox gradients collapse and subsequently recover remain poorly resolved. We investigated a mixing-restratification transition in Lake Shira (Siberia) with depth-stratified sampling of oxic, chemocline, anoxic, and water-sediment interface layers across four stages: intermittent holomictic (IH), complete holomictic (CH), developing meromictic (DM), and stable meromictic (M). 16S rRNA gene amplicons showed that CH homogenized the water column, dominated by Gamma- and Alphaproteobacteria, Campylobacteria, and Cyanobacteriia. As stratification re-formed (DM-M), communities became strongly depth-partitioned, with Desulfobacterota and other anaerobes re-established in sulfidic deep waters and assemblages concentrating near the redox transition. Nanopore metagenomics reconstructed 401 MAGs, revealing stage- and depth-specific functional repertoires consistent with redox zonation. Core MAGs, including Yoonia spp., persisted across phases, suggesting functional continuity underpinning rapid ecosystem recovery. These data provide a system-wide view of biogeochemical reassembly during collapse and restoration of stratification meromictic lake.

microbiology↗

bioRxiv2025

Bacteriophages of the predominant coral symbiont Endozoicomonas: novel models for coral holobiont interactions

Phages are important symbionts in corals that modulate the community and functions of other symbiotic bacteria. Although phages infecting coral pathogens have been reported, no phage targeting beneficial microorganisms in corals has been isolated to date. From seawater near Acropora and Stylophora corals, we isolated the first bacteriophages (designated EmPhiA and EmPhiS) that infect Endozoicomonas montiporae CL-33, a model strain of the coral-prevalent and predominant Endozoicomonas bacteria. Electron microscopic observations of both phages showed Myovirus-like morphology and head sizes characteristic of jumbophages, with cryo-electron microscopy reveals long whiskers unprecedent in known phages. Genetically, these phages shared 99.21% genome similarity and are distant from known prokaryotic viruses, suggesting that they represent a novel viral species, which we name Encorevirus taiwanensis, in a novel family Encoreviridae. The small burst sizes of these phages (13.14 PFU/cell for EmPhiA and 21.4 PFU/cell for EmPhiS) potentially enable continuous coexistence of them with host bacteria within corals, making them putative core members of coral holobionts. Furthermore, host range test showed that EmPhiA and EmPhiS infect both Endozoicomonas bacteria isolated from stony and soft corals, implying their presence in a broad spectrum of host marine invertebrates. Using EmPhiS, we also investigated phage-bacterium interaction during its infection of E. montiporae CL-33. Interestingly, in addition to modulation of host cellular machinery, we found expression of several tellurium resistance proteins by EmPhiS during infection, which may provide the host additional stress resistance. These phages provide a novel model that will greatly advance our understanding of coral-Endozoicomonas-phage interactions.

microbiology↗

bioRxiv2025

Unusual Ecofunctional Traits of Endozoicomonas: A Pan-Genomic Perspective

BackgroundEndozoicomonas is a widely distributed genus of marine bacteria, associated with various marine organisms, and recognized for its ecological importance in host health, nutrient cycling, and disease dynamics. Despite its significance, genomic features of Endozoicomonas remain poorly characterized due to limited availability of high-quality genome assemblies. ResultsIn this study, we sequenced 5 novel Endozoicomonas strains and re-sequenced 1 known strain to improve genomic resolution. By integrating these 6 high-quality genomes with 31 others that were publicly available, we identified a distinct, coral-associated clade not recognized by the previous two-clade classification. Pan-genomic analysis revealed significant variation in genetic trait distribution among clades. Notably, Endozoicomonas lacks quorum sensing capabilities, suggesting resistance to quorum quenching mechanisms. It also lacks the ability to synthesize and transport vitamin B12, indicating that it is not a primary source of this nutrient for holobionts. A remarkable feature of Endozoicomonas is its abundance of giant proteins, ranging from 15 to 65 kbp. We identified 92 such proteins, which clustered into three major groups based on amino acid similarity, each associated with specialized functions, such as antimicrobial synthesis, exotoxin production, and cell adhesion. Additionally, we explored prophages and CRISPR-Cas systems. We found that Endozoicomonas acquired prophages from diverse sources via infection or other types of gene transfer. Notably, CRISPR-Cas sequences suggest independent evolutionary trajectories from both prophage acquisition and phylogenetic lineage, implying a potential influence of geographic or environmental pressures. ConclusionsThis study provides new insights into the genomic diversity of Endozoicomonas and its genetic adaptation to diverse hosts. Identification of novel genomic features, including deficiencies in B12 synthesis and quorum sensing, the presence of giant proteins, prophages, and CRISPR-Cas systems, underscores its ecological roles in various holobionts. These findings open new avenues for research on Endozoicomonas and its ecological interactions.

ecology↗

bioRxiv2024

Spatiotemporal control of subcellular O-GlcNAc signaling using Opto-OGT

The posttranslational modification of intracellular proteins through O-linked {beta}-N-acetylglucosamine (O-GlcNAc) is a conserved regulatory mechanism in multicellular organisms. Catalyzed by O-GlcNAc transferase (OGT), this dynamic modification plays an essential role in signal transduction, gene expression, organelle function, and systemic physiology. Here we present Opto-OGT, an optogenetic probe that allows for precise spatiotemporal control of OGT activity through light stimulation. By fusing a photosensitive cryptochrome protein to OGT, Opto-OGT can be robustly and reversibly activated with high temporal resolution by blue light and exhibits minimal background activity without illumination. Transient activation of Opto-OGT results in mTORC activation and AMPK suppression which recapitulate nutrient-sensing signaling. Furthermore, Opto-OGT can be customized to be localized at specific subcellular sites. By targeting OGT to the plasma membrane, we demonstrate downregulation of site-specific AKT phosphorylation and signaling outputs in response to insulin stimulation. Thus, Opto-OGT is a powerful tool to define the role of O-GlcNAcylation in cell signaling and physiology.

cell biology↗

bioRxiv2020

Multiple Myeloma: Combination Therapy of BET Proteolysis Targeting Chimeric Molecule with CDK9 Inhibitor

Cyclin Dependent Kinase 9 (CDK9) associates with Bromodomain and Extra-Terminal Domain (BET) proteins to promote transcriptional elongation by phosphorylation of serine 2 of RNAP II C-terminal domain. We examined the therapeutic potential of selective CDK9 inhibitors (AZD 4573 and MC180295) against human multiple myeloma cells in vitro. Short-hairpin RNA silencing of CDK9 in Multiple Myeloma (MM) cell lines reduced cell viability compared to control cells showing the dependency of MM cells on CDK9. In order to explore synergy with the CDK9 inhibitor, proteolysis targeting chimeric molecule (PROTAC) ARV 825 was added. This latter drug causes ubiquitination of BET proteins resulting in their rapid and efficient degradation. Combination treatment of MM cells with ARV 825 and AZD 4573 markedly reduced their protein expression of BRD 2, BRD 4, MYC and phosphorylated RNA pol II as compared to each single agent alone. Combination treatment synergistically inhibited multiple myeloma cells both in vitro and in vivo with insignificant weight loss. The combination also resulted in marked increase of apoptotic cells at low dose compared to single agent alone. Taken together, our studies show for the first time that the combination of a BET PROTAC (ARV 825) plus AZD 4573 (CDK9 inhibitor) is effective against MM cells.

cancer biology↗

bioRxiv2017

Contribution of transition and stabilization processes to speciation is a function of the ancestral trait state and selective environment in Hakea

Currently the origin and trajectories of novel traits are emphasised in evolutionary studies, the role of stabilization is neglected, and interpretations are often post hoc rather than as hypothesised responses to stated agents of selection. Here we evaluated the impact of changing environmental conditions on trait evolution and stabilization and their relative contribution to diversification in a prominent Australian genus, Hakea (Proteaceae). We assembled a time-based phylogeny for Hakea, reconstructed its ancestral traits for six attributes and determined their evolutionary trajectories in response to the advent or increasing presence of fire, seasonality, aridity, nectar-feeding birds and (in)vertebrate herbivores/granivores. The ancestral Hakea arose 18 million years ago (Ma) and was broad-leaved, non-spinescent, insect-pollinated, had medium-sized, serotinous fruits and resprouted after fire. Of the 190 diversification events that yielded the 82 extant species analysed, 8-50% involved evolution, stabilization or re-evolution (reversal) of individual novel traits. Needle leaves appeared 14 Ma and increased through the Neogene/Quaternary coinciding with intensifying seasonality and aridity. Spinescence arose 12 Ma consistent with the advent of vertebrate herbivores. Bird-pollination appeared 14 Ma in response to advent of the Meliphagidae in the early Miocene. Small and large woody fruits evolved from 12 Ma as alternative defenses against granivory. Fire-caused death evolved 14 Ma, accounting for 50% of subsequent events, as fire became less stochastic. Loss of serotiny began in the late Miocene as non-fireprone habitats became available but only contributed 8% of events. Innovation and subsequent stabilization of functional traits promoted the overall species diversification rate in Hakea by 15 times such that only three species now retain the ancestral phenotype. Our approach holds great promise for understanding the processes responsible for speciation of organisms when the ancestral condition can be identified and the likely selective agents are understood.

ecology↗