Biology subjects

Lu, C.-Y.

Publications and source records attributed to Lu, C.-Y..

10 recordsLinked to original sources

bioRxiv2026

The missing part of the DMSP cycle in coral holobionts: Endozoicomonas exports acetate derived from DMSP degradation

Endozoicomonas, a dominant symbiotic bacterium in coral holobionts, is noted for its ability to degrade dimethylsulfoniopropionate (DMSP) so as to generate acetate. While acetate is a well-known short-chain fatty acid in metabolic cross-feeding relationships, it remains unclear whether acetate derived from bacterial DMSP degradation is available to corals and their other symbionts. In this study, we employed Endozoicomonas ruthgatesiae strain 8E (herein referred as 8E) as a model to examine availability of DMSP-derived acetate for other symbionts. Using gas chromatography-mass spectrometry (GC-MS), we observed a significant increase in acetate excretion in 8E upon exposure to DMSP. Stable isotope labeling further confirmed that this elevated acetate efflux originated directly from DMSP, suggesting a complete cycle of DMSP-derived carbon among coral symbionts. Transcriptomic analysis revealed that DMSP exposure upregulated dddD expression and triggered a systemic reconfiguration of metabolism, characterized by down-regulation of the TCA cycle and the Pta-AckA pathway, with carbon flux redirected to the glyoxylate shunt. These findings suggest that upon exposure to DMSP, metabolism of 8E shifts from biomass production to DMSP catabolism, resulting in acetate efflux. Notably, we found that elevated temperature diminishes DMSP cleavage activity of 8E, indicating thermal sensitivity of this bacterial metabolic activity. ImportanceEndozoicomonas is known for its dominance in coral holobionts and its ability to degrade DMSP, an important compound in the marine sulfur cycle. Acetate is one resulting product in microbial DMSP metabolism and a common cross-feeding molecule. Whether DMSP-derived acetate in coral-associated DMSP-degrading bacteria is employed for cross-feeding stands a critical step in making a complete carbon cycle of DMSP metabolism within coral holobionts. In this study, we employed GC-MS and RNA-sequencing techniques to offer the first evidence of acetate excretion in Endozoicomonas while metabolizing DMSP, as well as its underlying genetic mechanism. Furthermore, we demonstrate reduced genetic response and DMSP-degrading capability under an elevated temperature in Endozoicomonas ruthgatesiae strain 8E, the model bacterium employed in this study. These findings provide the missing puzzle of DMSP metabolism in coral holobionts and suggest a potential role of DMSP in modulating symbiotic interactions within coral holobionts.

microbiology↗

bioRxiv2025

Microbial profiling and single-cell transcriptomics reveal probiotic mechanisms of coral thermal resilience

Probiotics hold promise for enhancing coral resilience under climate-driven thermal stress, yet their mechanisms remain poorly understood. Here, we evaluate two Endozoicomonas species as coral probiotics and characterize their effects on microbial communities and host gene expression. We show that E. acroporae Acr-14T enhances thermal tolerance in Stylophora pistillata, suppresses opportunistic pathogens, and promotes beneficial microbes. To facilitate transcriptomic profiling, we assembled a chromosome-level genome of S. pistillata clade 1 (Pacific lineage) and used it to reveal that E. acroporae Acr-14T mitigates heat-induced protein-folding stress and supports host energy homeostasis. Single-cell transcriptomics further uncovered enhanced pro-survival signaling and modulation of the S-adenosylmethionine (SAMe) synthesis pathway. Together, our findings identify E. acroporae Acr-14T as a robust coral probiotic and provide mechanistic insights into host-microbe interactions that promote coral resilience under thermal stress.

microbiology↗

bioRxiv2025

Targeting Wnt Signaling and DNAJB6/MRJ-L as a Dual Anti-RSV Strategy: Insights into a Positive Regulatory Loop

Respiratory syncytial virus (RSV) is a major cause of severe respiratory infections, yet effective treatments are lacking. We found that the molecular chaperon DNAJB6/MRJ plays an essential role in RSV replication. Depletion of the long isoform of MRJ (MRJ-L) suppresses RSV replication. Transcriptomic analysis revealed that MRJ-L depletion downregulates Wnt signaling pathways. A pharmacological inhibitor of Wnt signaling suppressed RSV propagation and unexpectedly reduced MRJ-L expression, suggesting a positive regulatory loop between Wnt signaling and MRJ-L expression. Notably, simultaneous inhibition of Wnt signaling and MRJ-L additively suppressed RSV replication, suggesting that the Wnt-MRJ-L axis may serve as a new therapeutic target. This study provides insights into host-RSV interactions and potential antiviral strategies. Author SummaryThe molecular chaperone DNAJB6/MRJ has been implicated in the replication of respiratory syncytial virus (RSV), although the precise mechanisms remain unclear. In this study, we discovered that MRJ may influence RSV replication via Wnt signaling pathways. Specifically, we demonstrated that Wnt signaling inhibitor Wnt-C59 significantly reduced RSV replication by suppressing the synthesis of viral mRNA and genome/antigenome. Moreover, a positive feedback loop of the Wnt-MRJ axis may play a critical role in regulating RSV replication. Importantly, RSV replication was suppressed additively by inhibition of Wnt signaling and depletion of MRJ-L. Thus, a dual-targeted therapeutic approach may be effective in combating RSV infections.

pathology↗

bioRxiv2023

Successive responses of three coral holobiont components (coral hosts, symbiotic algae, and bacteria) to daily temperature fluctuations

Coral reef ecosystems support over a quarter of the worlds marine life and play important ecological and economic roles. However, the increasingly severe weather events associated with ocean warming and climate change are believed to be rapidly altering the functions of coral reefs and their ecosystems. Corals and their associated microbiota form a "holobiont," which includes symbiotic algae and other associated microbiota dominated by bacteria. These microbiota have a direct relationship with the health of the coral host. Their composition is influenced by various environmental factors, such as increasing sea water temperatures. Previous studies of the effects of temperature changes on coral physiology and associated bacterial communities have been conducted based on stable water temperatures set by mean temperatures, or by slowly increasing/decreasing temperatures. However, the daily temperature fluctuations that corals experience in nature are not stable. Rather, there may be significant differences of up to 6{degrees}C in a single day. The current understanding of the effects of large daily temperature fluctuations on coral and associated bacterial community dynamics is limited. Hence, in this study, we conducted a four-week tank experiment using different large daily temperature fluctuations accompanied by continuous warming conditions to investigate the effects on two common reef-building corals, Stylophora pistillata and Pocillopora acuta, in Taiwan. During the experiment, the activity of coral host catalase was measured, the photosynthetic ability of symbiotic algae was recorded, and the variation in bacterial communities was analyzed using the V6-V8 region of 16S rDNA. According to the results, different parts of the holobionts of different coral species exhibited varying response rates to the continuous warming conditions and diurnal temperature fluctuations. Additionally, it was found that diurnal temperature fluctuations may mitigate the heat stress on the host and reduce the changes in bacterial response to warming. Furthermore, the holobionts of different coral species may adopt different adaptation and survival strategies in response to diurnal temperature fluctuations and warming. Finally, based on the response of these two coral species under the conditions of diurnal temperature fluctuations and continuous warming, Acinetobacter and Rhodobacteraceae were identified as potential indicator coral-associated bacteria. This is the first study to investigate the tripartite dynamic response of coral, symbiotic algae and bacteria to daily temperature fluctuations.

microbiology↗

bioRxiv2021

Microbiome restructuring: dominant coral bacterium Endozoicomonas species display differential adaptive capabilities to environmental changes

Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the capacity of microbiome members to adapt to a new environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas related phylotypes belonging to two different species, including a novel species, Candidatus Endozoicomonas penghunesis 4G, whose chromosome level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species showed varied adaptation capabilities when coral colonies were transplanted in a new environment. The differential adaptation capabilities of dominant members of the microbiome can a) provide distinct advantages to coral hosts when subjected to changing environmental conditions and b) have positive implications for future reefs.

microbiology↗

bioRxiv2021

Response of Endozoicomonas montiporae to heat stress and coral host lysates

Endozoicomonas, a core bacterial group in corals, may also be a coral symbiont. Endozoicomonas communities often decrease rapidly in corals under heat stress. However, how the bacteria respond to changes in temperature and coral host during heat stress is unknown. Here, we employed the cultivable, dominant species E. montiporae as a working organism to explore how Endozoicomonas responds to heat stress. We designed two experiments to clarify the extent to which E. montiporae is influenced by temperature and coral host. We detected differentially expressed protein (DEP) profiles in this bacterium at 31{degrees}C and 33{degrees}C compared to 25{degrees}C by tandem mass tags-based quantitative proteome analysis. Fifty DEPs, including many heat shock proteins, were detected when the temperature changed. The expression of antioxidant defense proteins and key pyruvate synthase proteins decreased, suggesting that E. montiporae were in a physiology of stress at 33{degrees}C. Furthermore, some proteins were differentially expressed because of the heat-stress-treated coral lysate specifically, suggesting that not only heat but also heat-induced host factors can affect the protein expression of the bacterium. This study provides an in-depth analysis of how the molecular mechanisms of Endozoicomonas are affected by heat stress and coral host.

microbiology↗

bioRxiv2021

Endothelial integration of mechanosensory signals by the spectrin cytoskeleton

Physiological blood flow induces the secretion of vasoactive compounds, notably NO, and promotes endothelial cell elongation and reorientation parallel to the direction of applied shear. How shear is sensed and relayed to intracellular effectors is incompletely understood. We demonstrate that an apical spectrin network is essential to convey the force imposed by shear to endothelial mechanosensors. By anchoring CD44, spectrin modulates the cell surface density of hyaluronan, which senses and translates shear into changes in plasma membrane tension. Spectrins also regulate the stability of apical caveolae, where the mechanosensitive Piezo1 channels are thought to reside. Accordingly, shear-induced Piezo1 activation and the associated calcium influx were absent in spectrin-deficient cells. As a result, cell realignment and flow-induced eNOS stimulation were similarly dependent on spectrin. We concluded that the apical spectrin network is not only required for shear sensing, but transmits and distributes the resulting tensile forces to mechanosensors that elicit protective and vasoactive responses.

cell biology↗

bioRxiv2020

The fate of standing variation and new mutation under climate change

Many species face existence threat under anthropogenic climate change, and standing genetic variation was proposed as a way for sessile species to adapt to novel environments. However, it is still unknown whether standing genetic variants, being adaptive to current environmental variability, are sufficient to guarantee future survival. Here we investigate the relative importance of standing variation versus new mutations from the past to infer their future fate in nature. In the wild banana species Musa itinerans where the Taiwanese populations were ancient immigrants from the Chinese populations, new mutations exert larger effect size in precipitation-related variables, where Taiwan contains extreme environments beyond the ancestral climatic range, and new alleles have stronger association with novel environments. For temperature-related variables where Taiwan is within the ancestral climatic range, standing variants are more important than new mutations. The effect sizes of adaptive variants therefore differ under distinct environmental pressures, supporting theoretical predictions that natural selection favors new mutations with larger effect sizes in novel environments where the population is far from the adaptive peak. Despite their importance, large-effect variants also have higher mismatch and may be more vulnerable to future environmental perturbation, leaving minor-effect variants the main source of adaptive response to rapid anthropogenic climate change. Our work provides a support in natural environment to the previous conclusions from theoretical modeling and microbial experiments in well-controlled lab conditions.

evolutionary biology↗

bioRxiv2019

A genomic view of coral-associated Prosthecochloris and a companion sulfate-reducing bacterium

Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic microorganisms, research on the roles of endolithic anaerobic microorganisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated Prosthecochloris (CAP), a genus of anaerobic green sulfur bacteria, was dominant in the skeleton of the coral Isopora palifera. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living Prosthecochloris. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new near-complete CAP genomes--Candidatus Prosthecochloris isoporaea and Candidatus Prosthecochloris sp. N1--from coral Isopora palifera endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other Prosthecochloris and harbor several CAP-unique genes. Interestingly, different CAP species harbor various pigment synthesis and sulfur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel near-complete SRB genome--Candidatus Halodesulfovibrio lyudaonia--was also recovered from the same culture. The fact that CAP and various sulfate-reducing bacteria (SRB) co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of Ca. P. sp. N1 and Ca. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton. ImportanceLittle is known about the ecological roles of endolithic microbes in the coral skeleton; one potential role is as a nutrient source for their coral hosts. Here, we identified a close ecological relationship between CAP and SRB. Recovering novel near-complete CAP and SRB genomes from endolithic cultures in this study enabled us to understand the genomic and metabolic features of anaerobic endolithic bacteria in coral skeletons. These results demonstrate that CAP members with similar functions in carbon, sulfur, and nitrogen metabolisms harbor different light-harvesting components, suggesting that CAP in the skeleton adapts to niches with different light intensities. Our study highlights the potential ecological roles of CAP and SRB in coral skeletons and paves the way for future investigations into how coral endolithic communities will respond to environmental changes.

microbiology↗

bioRxiv2019

Dominant coral bacterium Endozoicomonas acroporae metabolizes DMSP

Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral-sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase--a dddD gene homolog found in all E. acroporae strains--and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.

ecology↗