Biology subjects

Sandgren, M.

Publications and source records attributed to Sandgren, M..

6 recordsLinked to original sources

bioRxiv2025

Titania Nanoparticle Regulate Innate Immunity

In-vivo studies on wound healing have shown that small metal oxide nanoparticles (NPs), such as titania, ferria, and alumina, promote wound closure, likely by enhancing blood coagulation and via activation of the contact system. However, titania differs from the others as it supports the regrowth of normal skin tissue without scarring. This unique effect was hypothesised to result from its ability to suppress inflammation, possibly by interfering with the complement system. Ex-vivo whole blood experiments within the present study confirm that titania NPs significantly dampen the immune response and surface plasmon resonance (SPR) biosensor analysis confirms that the nanoparticle binds with nanomolar affinity to complement C3, a central protein in the human innate immune system. To elucidate the molecular basis of this effect, we developed a novel cryo-electron microscopy (cryo-EM) methodology capable of resolving the challenging interface between metal NPs and proteins. This approach revealed that TiO{square} binds with high specificity to a single domain on C3. The NP restricts the conformational dynamics of C3 and thus blocks the initiation of the complement cascade. These structural and biophysical insights support the biochemical findings and previous observations within the contact system. Our method advancement demonstrates that cryo-EM can uncover physiologically relevant interactions between proteins and nanomaterials at high resolution and offers a strong foundation for others investigating metal-biological interactions.

biochemistry↗

bioRxiv2025

A glycerol oxidase from Norway spruce (Picea abies L. Karst.) expands biochemical and structural attributes of the GMC oxidoreductase superfamily

O_LIInvestigations to uncover the versatility of carbohydrate active enzymes belonging to the auxiliary activity family 3 (AA3) have focused on microbial enzymes. Plant genomes also harbor AA3 encoding genes, and reverse genetics approaches have shown their importance in plant development. To date, however, detailed biochemical characterizations and structures of plant AA3 enzymes have not been reported. C_LIO_LIHere, we describe screening AA3 encoding genes from Norway spruce and the first in-depth biochemical and structural characterization of a plant AA3 oxidase, PaAOX1. PaAOX1 was crystallized, and the structure was solved by X-ray crystallography. C_LIO_LIPaAOX1 demonstrated highest oxidase activity against glycerol. It oxidized glycerol to glyceraldehyde, then further to glyceric acid, and showed preference for L-glyceraldehyde over D-glyceraldehyde. Despite the low sequence similarity with fungal alcohol oxidases, it had all the structural features of the typical AA3 enzyme. C_LIO_LIPaAOX1 has a novel activity among the characterized AA3s, and it showed a new structural arrangement of the region surrounding the catalytic center. Our findings contribute to a deeper understanding of the structural and functional aspects of enzymes in the GMC superfamily, and especially of alcohol oxidases, expanding the knowledge from fungi to plants. C_LI

biochemistry↗

bioRxiv2021

SPIRO-the automated Petri plate imaging platform designed by biologists, for biologists

Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photos of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIROs excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared to manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing and photoblastic response.

plant biology↗

bioRxiv2020

Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases

Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, comprised of a catalytic domain attached to a carbohydrate binding module (CBM) via a flexible linker, and exhibit a long active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical biological and industrial importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, using the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy. The lengths of the A4, B2, B3, and B4 loops were strongly correlated with functional subtype across the GH7 family. Position-specific classification rules were derived such that specific amino acids at 42 different sequence positions predicted the functional subtype with accuracies greater than 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. We propose these positions play vital roles in the functional variation of GH7 cellulases. Taken together, our results complement numerous experimental findings and present functional relationships that can be applied when prospecting GH7 cellulases from nature, for sequence annotation, and to understand or manipulate function.

bioinformatics↗

bioRxiv2019

Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipidproduction

BackgroundRhodotorula toruloides is a promising platform organism for production of lipids from lignocellulosic substrates. Little is known about the metabolic aspects of lipid production from the lignocellolosic sugar xylose by oleaginous yeasts in general and R. toruloides in particular. This study presents the first proteome analysis of the metabolism of R. toruloides during conversion of xylose to lipids.\n\nResultsR. toruloides cultivated on either glucose or xylose was subjected to comparative analysis of its growth dynamics, lipid composition, fatty acid profiles and proteome. The maximum growth and sugar uptake rate of glucose-grown R. toruloides cells were almost twice that of xylose-grown cells. Cultivation on xylose medium resulted in a lower final biomass yield although final cellular lipid content was similar between glucose- and xylose-grown cells. Analysis of lipid classes revealed the presence of monoacylglycerol in the early exponential growth phase as well as a high proportion of free fatty acids. Carbon source-specific changes in lipid profiles were only observed at early exponential growth phase, where C18 fatty acids were more saturated in xylose-grown cells. Proteins involved in sugar transport, initial steps of xylose assimilation and NADPH regeneration were among the proteins whose levels increased the most in xylose-grown cells across all time points. The levels of enzymes involved in the mevalonate pathway, phospholipid biosynthesis and amino acids biosynthesis differed in response to carbon source. In addition, xylose-grown cells contained higher levels of enzymes involved in peroxisomal beta-oxidation and oxidative stress response compared to cells cultivated on glucose.\n\nConclusionsThe results obtained in the present study suggest that sugar import is the limiting step during xylose conversion by R. toruloides into lipids. NADPH appeared to be regenerated primarily through pentose phosphate pathway although it may also involve malic enzyme as well as alcohol and aldehyde dehydrogenases. Increases in enzyme levels of both fatty acid biosynthesis and beta-oxidation in xylose-grown cells was predicted to result in a futile cycle. The results presented here are valuable for the development of lipid production processes employing R. toruloides on xylose-containing substrates.

microbiology↗

bioRxiv2019

Genome-scale model of Rhodotorula toruloides metabolism

The basidiomycete red yeast Rhodotorula toruloides is a promising platform organism for production of biooils. We present rhto-GEM, the first genome-scale model of R. toruloides metabolism, that was largely reconstructed using RAVEN toolbox. The model includes 4869 genes, 897 reactions, and 3334 metabolites. Lipid metabolism was described using the SLIMEr formalism, which allows direct integration of lipid class and acyl chain experimental distribution data. The simulation results confirmed that the R. toruloides model provides valid growth predictions on glucose, xylose and glycerol, while prediction of genetic engineering targets to increase production of linolenic acid and triacylglycerols highlighted genes that have previously been successfully used to increase lipid production. This renders rtho-GEM useful for future studies to improve the production of other industrially important oleochemicals including both value-added fatty acids and carotenoids, while it will also be valuable tool for system-wide omics-data analysis in R. toruloides. Expanding the portfolio of GEMs for lipid accumulating fungi contributes to both understanding of metabolic mechanisms of the oleaginous phenotype but also uncover particularities of lipid production machinery in R. toruloides.

systems biology↗