Biology subjects

Trinh, L.

Publications and source records attributed to Trinh, L..

3 recordsLinked to original sources

bioRxiv2025

Role of Dienelactone Hydrolases in PET Biodegradation by Flavobacteria Maribacter dokdonensis and Arenibacter palladensis

Dienelactone hydrolases (DLHs, EC 3.1.1.45) are enzymes that play a crucial role in the breakdown of cyclic esters and some have been found to act on substrates such as terephthalate esters, which are monomers of polyethylene terephthalate (PET). In the current study, we show that bacteria affiliated with the Bacteroidota (class Flavobacteria) harbor DLHs acting on PET foil and powder. We report on the isolation of two marine bacterial strains, Arenibacter palladensis UHH-Hm9b and Maribacter dokdonensis UHH-5R5, forming biofilms on PET foil and releasing {micro}M amounts of terephthalic acid after 5-7 days. Genome sequencing and functional analyses identified two secreted DHLs designated PET93 and PET 94 involved in PET degradation. While their predicted active sites and substrates binding pockets were identical to previously published PETases, both enzymes differed largely in their structural features from known PETases and represent novel scaffolds. Further they lacked the typical porC-domain of the known PETases from the Flavobacteria. Biochemical characterization of the two recombinant enzymes confirmed activity on PET, the primary degradation products Bis(2-Hydroxyethyl) terephthalate (BHET) and Mono-(Hydroxyethyl) terephthalate (MHET). These are the first DLHs to be reported being active on plastics and our findings indicate that Flavobacteria harbor an unexpectedly wide range of PET-active promiscuous enzymes. IMPORTANCEGlobal plastics pollution is a major environmental challenge, and we still have limited knowledge of marine microbiota involved in possible remediation. Our research shows that marine Flavobacteria harbor the potential for PET degradation using dienelactone hydrolases (DLHs, EC 3.1.1.45). The widespread distribution of these microorganisms and the notion that these enzymes are secreted may imply a possible role in marine PET remediation.

microbiology↗

bioRxiv2025

SpatialAgent: An Autonomous AI Agent for Spatial Biology

Advances in AI are transforming scientific discovery, yet spatial biology, a field that deciphers the molecular organization within tissues, remains constrained by labor-intensive workflows. Here, we present SpatialAgent, an autonomous AI agent for spatial biology research. SpatialAgent couples large language models with a Plan-Act-Conclude architecture, dynamic tool and skill retrieval, multimodal interpretation, and verification modules that audit generated claims. It supports the full discovery loop, from gene-panel design and multimodal annotation to trajectory inference, cell-cell communication analysis, imputation, and hypothesis generation. Across human and mouse brain, heart, tonsil, colon, and prostate datasets, SpatialAgent outperformed established computational baselines and matched or surpassed expert scientists in key tasks. In open-ended case studies, it recovered known tissue organization and generated spatially grounded hypotheses. In a prospective mouse prostate cancer Xenium study, it designed a compact 100-gene add-on panel that profiled 4.2 million cells across 21 samples, improved cell-type and malignant-state prediction, and captured spatially structured tumor and microenvironment programs. SpatialAgent establishes a framework for autonomous and collaborative discovery in spatial biology.

bioinformatics↗

bioRxiv2025

Polyethylene terephthalate (PET) primary degradation products affect c-di-GMP-, cAMP-signaling and quorum sensing (QS) in Vibrio gazogenes DSM 21264

Global plastic pollution in oceans and estuaries is increasing rapidly and its well known that bacteria colonize plastic particles of all sizes. Vibrio spp. are frequently found as part of the plastisphere. We recently showed that Vibrio gazogenes DSM 21264 harbors a promiscuous esterase designated PET6. We now provide evidence that the pet6 gene is expressed under a wide range of environmental conditions in its native host. However, in PET- and PE-grown biofilms the pet6 gene expression was not affected by the type of surface. The pet6 transcription was sufficient to allow enzyme production and release of {micro}M amounts of mono-(2-hydroxyethyl) terephthalate (MHET) and terephthalic acid (TPA) already after 24 hours of incubation on PET foil. Notably, the highest pet6 gene transcription was observed in planktonic lifestyle in the presence of bis(2-hydroxyethyl) terephthalate (BHET) one of the primary degradation products of PET. BHET was further hydrolyzed by PET6 and UlaG, a lactonase that had not been known to be involved in BHET degradation. Elevated concentrations of BHET affected the major signaling circuits involved in bacterial quorum sensing (QS), c-di-GMP and cAMP-CRP signaling. This resulted in failure to form biofilms, synthesis of the red pigment prodigiosin and altered colony morphologies. While BHET had a very wide impact, TPA interfered mainly with the bacterial QS by attenuating the expression of the CAI-I autoinducer synthase gene. These observations imply a potential role of BHET and TPA as nutritional signals in Vibrio gazogenes and that may affect its growth and survival in the plastisphere. IMPORTANCEThis study provides first evidence that Vibrio gazogenes DSM 21264 secretes an active PET hydrolase and degrades the polymer using PET6 when growing in biofilms on foils and microplastic particles. The study further provides evidence that the primary PET degradation products BHET and TPA may have a profound impact on the global QS, c-di-GMP and cAMP-CRP signaling of V. gazogenes and its capability to colonize plastic particles in the marine environment.

microbiology↗