Biology subjects

Perez-Garcia, P.

Publications and source records attributed to Perez-Garcia, P..

6 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

A Combined Chemo-Enzymatic Treatment for the Oxidation of Epoxy-Based Carbon Fiber-Reinforced Polymers (CFRPs)

Carbon fiber-reinforced polymers (CFRPs), particularly epoxy-based composites, have become essential in the aerospace, automotive, and wind energy industries due to their robust mechanical properties, and lightweight nature. However, there is a lack of recycling technologies that are environmentally sustainable while also ensuring the recovery of carbon fibers in their original state. Although certain bacterial and fungal strains can colonize epoxy polymers, enzymes capable of efficiently degrading these materials have not yet been reported. Consequently, there is an urgent need for an effective, sustainable, and biologically inspired solution for CFRP recycling. Here, a chemo-enzymatic two-step oxidation process was developed. A chemical pre-treatment with propionic acid and hydrogen peroxide was used to recover imbedded carbon fibers. Additionally, three novel bacterial laccases isolated from the European spruce bark beetle (Ips typographus) demonstrated the ability to degrade three epoxy resin scaffolds from Hexflow(R) RTM6, used in aircraft applications. The sequential combination of both oxidative steps enabled the retrieval of clean carbon fibers and partial modification of epoxy functional groups, with the release of defined products over time. This bio-inspired approach renders the process more environmentally friendly and marks an initial step toward developing a bio-based recycling method for epoxy CFRPs.

biochemistry↗

bioRxiv2024

UNVEILING STEM CELL INDUCTION MECHANISMS FROM SPATIOTEMPORAL CELL-TYPE-SPECIFIC GENE REGULATORY NETWORKS IN POSTEMBRYONIC ROOT ORGANOGENSIS

Plants grow continuously by developing new organs, a complex process that requires the formation of specific and functional tissue patterns. Tap root systems, as observed in Arabidopsis thaliana, undergo lateral root formation, a developmental mechanism that necessitates the establishment of stem cell lineages. However, the underlying mechanisms remain poorly understood. We have reconstructed a spatiotemporal cell-type-specific transcriptional map of early lateral root organogenesis in Arabidopsis, profiling single and double fluorescent markers across 8 different cell types in the root stem cell lineage. Employing dynamic Bayesian network inference, based on time-course experiments and developmental time, alongside tree-based methods, we investigated lineage developmental progression and precursor stem-cell specification. Our results reveal a morphogenic cascade of hierarchical interdependent transcription factors driving stem cell initiation, and identify the QC/Endodermis transitioning cells as root stem cell progenitors. The associated formative program involves a profound transcriptomic re-arrangement, which, remarkably, precedes the activation of known stem-cell transcriptional signatures. Our data support a model in which root-stem-cell networks do not initiate stem formation, although various stem cell regulators are involved. Collectively, our study identifies core transcriptional signatures associated with stem cell induction and elucidates the dynamic regulatory mechanism driving early stem cell lineage establishment.

developmental biology↗

bioRxiv2023

GNOM-Dependent Endosomal Recycling Sets the Timing of Founder Cell Specification

1.Lateral root growth occurs from primed xylem pole pericycle cells that can be specified as founder cells, but how these cells acquire the pluripotency state to initiate a root organogenesis program is not fully understood. Here, we find that the EMS 204 mutant is unable to specify founder cells due to a point mutation affecting the C-terminal HDS3 domain of the GNOM protein. We used genetics and cell biology to study the trafficking machinery of xylem pole pericycle cells, cells in which GNOM is primarily associated with recycling endosomes. We found that the lack of the HDS3 domain negatively affects the stability of the GNOM protein within the cells of the xylem pole pericycle and, subsequently, the integrity of the trafficking machinery of these cells. We determined that GNOM is responsible for the recycling of AUX1 toward the plasma membrane at the xylem pole pericycle and impairment of this recycling results in premature accumulation of AUX1 in the vacuole. In this work, we describe a cell type-specific cellular mechanism and the role of a particular domain during lateral root development.

plant biology↗

bioRxiv2022

The first archaeal PET-degrading enzyme belongs to the feruloyl-esterase family

Polyethylene terephthalate (PET) is a commodity polymer known to globally contaminate marine and terrestrial environments. Today, around 40 bacterial and fungal PET-active enzymes (PETases) are known, originating from four bacterial and two fungal phyla. In contrast, no archaeal enzyme has been identified to degrade PET. Here we report on the structural and biochemical characterization of PET46, an archaeal promiscuous feruloyl esterase exhibiting degradation activitiy on PET, bis-, and mono-(2-hydroxyethyl) terephthalate (BHET and MHET). The enzyme, found by a sequence-based metagenome search, was derived from a non-cultivated, deep-sea Candidatus Bathyarchaeota archaeon. Biochemical characterization demonstrated that PET46 is a promiscuous, heat-adapted hydrolase. Its crystal structure was solved at a resolution of 1.71 [A]. It shares the core alpha/beta-hydrolase fold with bacterial PETases, but contains a unique lid common in feruloyl esterases, which is involved in substrate binding. Thus, our study significantly widens the currently known diversity of PET-hydrolyzing enzymes, by demonstrating PET depolymerization by a lignin-degrading esterase.

biochemistry↗

bioRxiv2019

Stem Cell Activity And Regeneration In Roots Require Non-Cell Autonomous Regulation From The Ground Tissue

Stem cells are central to plant development. During root postembryonic development stem cells generating tissues are patterned in layers around a stem cell organizer or quiescent center (QC). How stem cell lineages are initially patterned is unclear. Here, we describe a role for BLUEJAY (BLJ), JACKDAW (JKD) and SCARECROW (SCR) transcription factors in patterning of cell lineages during growth and in patterning reestablishment during regeneration through regulation of number of QC cells and their regenerative capacities. In blj jkd scr mutants, QC cells are progressively lost which results in loss of tissue layers. Upon laser ablation blj jkd scr is impaired in QC division and specification resulting in severe impairment in pattern regeneration. Beyond direct regulation of QC activity by these transcription factors, reduced levels of SHORT-ROOT (SHR) and of PIN auxin transporters were observed in the vasculature of blj jkd scr, leading to strong reduction in the auxin response in the QC. We narrowed down non-cell-autonomous regulation of vascularly expressed genes in blj jkd scr to C-REPEAT BINDING FACTOR 3 (CBF3). cbf3 mutant shows reduced levels of SHR in the vasculature, and in addition QC disorganization and downregulation of the QC regulator WUSCHEL-RELATED HOMEODOMAIN 5 (WOX5). CBF3 gene is primarily expressed in the ground tissue downstream of BLJ, JKD and SCR, while CBF3 protein may move. Targeted-expression of CBF3 to the ground tissue of blj jkd scr recovers radial patterning and regeneration. We propose that BLJ, JKD and SCR regulate QC-mediated patterning, and that part of this regulation involves CBF3.

developmental biology↗