Biology subjects

Benedetti, M.

Publications and source records attributed to Benedetti, M..

7 recordsLinked to original sources

bioRxiv2024

The reducing end of cell wall oligosaccharides is critical for DAMP activity in Arabidopsis thaliana and can be exploited by oligosaccharide oxidases in the scavenging of phenolic radicals.

O_LIThe enzymatic hydrolysis of cell wall polysaccharides results in the production of oligosaccharides with nature of damage-associated molecular patterns (DAMPs) that are perceived by plants as danger signals. In vitro, the oxidation of oligogalacturonides and cellodextrins by plant FAD-dependent oligosaccharide-oxidases (OSOXs) suppresses their elicitor activity, suggesting a protective role of OSOXs against a prolonged activation of defense responses potentially deleterious for plant health. However, OSOXs are also produced by phytopathogens and saprotrophs, complicating the understanding of their role in plant-microbe interactions. C_LIO_LIThe oxidation catalyzed by specific fungal OSOXs also converts the elicitor-active cello-tetraose and xylo-tetraose into elicitor-inactive forms, indicating that the oxidation state of cell wall oligosaccharides is crucial for their DAMP function, irrespective of whether the OSOX originates from fungi or plants. C_LIO_LICertain OSOXs can transfer the electrons from the reducing end of these oligosaccharides to phenolic radicals instead of molecular O2, highlighting an unexpected sub-functionalization of these enzymes. C_LIO_LIThe activity of OSOXs may be crucial for a thorough understanding of cell wall metabolism since these enzymes can redirect the reducing power from sugars to phenolic components of the plant cell wall, an insight with relevant implications for both plant physiology and green technologies. C_LI

plant biology↗

bioRxiv2024

Berberine Bridge enzyme-like oxidases orchestrate homeostatic control and signaling of oligogalacturonides in defense and wounding

Plant immunity is triggered by endogenous elicitors known as damage-associated molecular patterns (DAMPs). Oligogalacturonides (OGs) are DAMPs released from the cell wall (CW) demethylated homogalacturonan during microbial colonization, mechanical or pest-provoked tissue damage, and physiological CW remodeling. Berberine Bridge Enzyme-like (BBE-l) proteins named OG oxidases (OGOXs) have been proposed to govern OGs homeostasis, which is necessary to avoid deleterious growth-affecting hyper-immunity and possible cell death. Using OGOX1 over-expressing lines and ogox1/2 double mutants, we show that these enzymes determine the levels of active OGs vs. inactive oxidized products (oxOGs). The ogox1/2-deficient plants have elevated levels of OGs, while plants overexpressing OGOX1 accumulate oxOGs. The balance between OGs and oxOGs affect disease resistance against Pseudomonas syringae pv tomato, Pectobacterium carotovorum, and Botrytis cinerea depending on the microbial capacity to respond to OGs and metabolize oxOGs. Gene expression upon plant infiltration with OGs reveals that OGOXs orchestrate OG signaling in defense as well as upon tissue damage, pointing to these enzymes as apoplastic players in immunity and tissue repair. TeaserOxidases control the homeostasis of oligogalacturonides in the cell wall and play a pivotal role in the plant immunity.

plant biology↗

bioRxiv2023

Reprogramming method does not impact the neuronal differentiation potential of 16p11.2 deletion patient iPSCs

A major impediment to the actualization of the induced pluripotent stem cell (iPSC)-based personalized medicine revolution is the lack of widely accepted standard operating procedures (SOPs) across different groups and institutions. The various methods employed can include choice of starting materials, reprogramming agents, and culture conditions, with each of these factors hypothesized to influence the reprogramming efficiency and transcriptional identity of iPSCs. As such, we systematically compared iPSC reprogramming procedures using cells derived from the somatic cells of three patients with 16p11.2 deletion syndrome (16p11.2del) and found remarkable similarity among the different methods. FACS analysis revealed that regardless of somatic cell type (fibroblast, lymphocyte, erythroblast), route of reprogramming factor introduction (mRNA, Sendai virus, episome), donor sex, or facility (Rutgers, NYSCF), 16p11.2del patient iPSCs were viable as high purity cultures expressing pluripotency marker proteins. This observation was supported at the transcript level by qPCR analysis, which demonstrated the ability for the iPSCs to differentiate into all three embryonic germ cell lineages after 12 days in culture as embryoid bodies. NGN2-mediated differentiation of these iPSCs produced functional neurons that formed active synaptic networks as revealed by multi-electrode array (MEA) recordings. Importantly, no group-wise comparisons among the reprogramming methods yielded consistent statistically significant differences, indicating that these procedures are equally capable of producing pluripotent stem cells that can efficiently differentiate into mature, functional neurons. This work highlights the utility of these reprogramming methods and supports the use of differentially reprogrammed iPSCs for direct comparative studies of human neurodevelopment.

developmental biology↗

bioRxiv2023

BERBERINE BRIDGE ENZYME-LIKE OXIDASES OF CELLODEXTRINS AND MIXED-LINKED β-GLUCANS CONTROL SEED COAT FORMATION

A member of the Arabidopsis Berberine Bridge Enzyme-like (BBE-l) protein family named CELLODEXTRIN OXIDASE 2 (CELLOX2) has been characterized in this paper and shown to display structural and enzymatic features similar to the previously characterized CELLOX1. These include the capability to oxidize the mixed-linked {beta}-1[->]3/{beta}-1[->]4-glucans (MLGs), recently described as cell wall-derived damage-associated molecular patterns (DAMPs) that activate plant immunity. The two paralogous genes show a different expression profile. Unlike CELLOX1, CELLOX2 is not expressed in seedlings or in adult plants and is not involved in immunity against Botrytis cinerea. Both genes are expressed in a concerted manner in the seed coat during development: whereas CELLOX2 transcripts are detected mainly during the heart stage, CELLOX1 transcripts are detected later, when the expression of CELLOX2 decreases. Analysis of seeds of cellox1 and cellox2 knock-out mutants show alterations in the structure of the coat and mucilage, but not in their monosaccharide composition. We propose that the cell wall structure of specific organs is not only the result of a coordinated synthesis/degradation of polysaccharides but also of their exposure to enzymatic oxidation. Our results also reinforce the view that the family of BBE-l proteins is at least in part devoted to the control of the activity of cell wall-derived oligosaccharides acting as DAMPs. SENTENCETwo Arabidopsis BBE-like oxidases of the cell wall DAMPs cellodextrins and mixed-linked {beta}-glucans inactivate their elicitor activity. Seed coat and mucilage are altered in null mutants of two enzymes.

plant biology↗

bioRxiv2022

RADICAL CATION SCAVENGING ACTIVITY OF BERBERINE BRIDGE ENZYME-LIKE OLIGOSACCHARIDE OXIDASES ACTING ON SHORT CELL WALL FRAGMENTS.

Oligogalacturonide-oxidases (OGOXs) and cellodextrin-oxidase (CELLOX) are plant berberine bridge enzyme-like oligosaccharide-oxidases (OSOXs) that oxidize, respectively, oligogalacturonides (OGs) and cellodextrins (CDs), thereby inactivating their elicitor nature and concomitantly releasing H2O2. Little is known about the physiological role of OSOX activity. By using an ABTS*+-reduction assay, we identified a novel reaction mechanism through which the activity of OSOXs on cell wall oligosaccharides scavenged the radical cation ABTS*+ with an efficiency dependent on the type and length of the oxidized oligosaccharide. In contrast to the oxidation of longer oligomers such as OGs (degree of polymerization from 10 to 15), the activity of OSOXs on short galacturonan- and cellulose-oligomers (degree of polymerization [≤] 4) successfully counteracted the radical cation-generating activity of a fungal laccase, suggesting that OSOXs can generate radical cation scavenging activity in the apoplast with a power proportional to the extent of degradation of plant cell wall, with possible implications for redox homeostasis and defense against oxidative stress.

plant biology↗

bioRxiv2022

Berberine Bridge Enzyme-Like Oligosaccharide Oxidases Act As Enzymatic Transducers Between Microbial Glycoside Hydrolases And Plant Peroxidases

OG-oxidases (OGOXs) and CD-oxidase (CELLOX) are plant berberine bridge enzyme-like oligosaccharide oxidases that oxidize oligogalacturonides (OGs) and cellodextrins (CDs), cell wall fragments with nature of damage-associated molecular patterns (DAMPs). The oxidation of OGs and CDs attenuates their elicitor activity by concomitantly releasing H2O2. Here, we demonstrate that the H2O2 generated downstream of the combined action between a fungal polygalacturonase and OGOX1 or an endoglucanase and CELLOX can be directed by plant peroxidases (PODs) either towards a reaction possibly involved in plant defence such as the oxidation of monolignol or a reaction possibly involved in a developmental event such as the oxidation of auxin (IAA), pointing to OGOX1 and CELLOX as enzymatic transducers between microbial glycoside hydrolases and plant PODs.

plant biology↗

bioRxiv2021

SPIN - Species by Proteome INvestigation

Genetic species determination has become an indispensable tool in forensics, archaeology, ecology, and food authentication. The available methods are either suited for detecting a single taxon across many samples or for screening a wide range of species across a few samples. Here, we introduce "Species by Proteome INvestigation" (SPIN), a proteomics workflow capable of querying over 150 mammalian species in 7.2 minutes of mass spectrometry (MS) analysis. Streamlined and automated sample preparation by protein aggregation capture, high-speed chromatography and data-independent acquisition, and a confident species inference algorithm facilitate processing hundreds of samples per day. We demonstrate the correct classification of known references, reproducible species identification in degraded Iron-Age material from Scandinavia, and test the limits of our methods with Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable with other biological tissues and taxa.

biochemistry↗