Biology subjects

Sandholm, R. M.

Publications and source records attributed to Sandholm, R. M..

3 recordsLinked to original sources

bioRxiv2025

Discovery and characterization of bacterial unspecific peroxygenase-like heme-thiolate enzymes

Unspecific peroxygenases (UPOs, EC. 1.11.2.1) are promising biocatalysts for the oxyfunctionalization of organic molecules and the synthesis of industrially relevant compounds due to their vast repertoire of catalyzed reactions. To date, thousands of putative UPO genes have been identified in eukaryotic genomes, most of them in the Ascomycota and Basidiomycota phyla, and several UPOs have been characterized. Remarkably, no related enzymes have ever been reported in prokaryotic organisms. Here, we describe the discovery of a novel family of diverse bacterial heme-thiolate peroxygenases through structure database mining, followed by functional characterization of selected representatives. The bacterial UPO-like proteins (BUPOs) are structurally analogous to family I ("short") fungal UPOs, despite having sequence similarity below 20%. Expression of one of these proteins (HydBUPO) in its native host (Hydrogenophaga sp. A37) was confirmed by proteomics. Several BUPOs were cloned and expressed in Escherichia coli. In biochemical assays, the BUPOs were able to catalyze one-electron oxidation (peroxidase activity) of ABTS and 2,6-dimethoxyphenol, and two-electron oxidation (peroxygenase activity) of naphthalene, indole, 3-phenyl-1-propanol and 16-hydroxypalmitic acid, using hydrogen peroxide as co-substrate. These enzymes thus represent a new family of bacterial heme-thiolate peroxygenases that share structural and functional features with eukaryotic UPOs, offering new potential candidates for developing industrially relevant biocatalysts.

biochemistry↗

bioRxiv2025

Microbial degradation of a widely used model polyethylene is restricted to medium- and long-chain alkanes and their oxidized derivatives

Plastics are widely used materials, yet their chemical stability hinders biodegradation, exacerbating pollution on a global scale. Soils contaminated with plastic may foster microbes adapted to degrade plastics or plastic derivatives, and these organisms and their enzymes offer promising avenues for the development of biotechnological recycling strategies. Here, two microbial communities originating from soil collected at a plastic-contaminated landfill in Norway were enriched to select for bacteria involved in the decomposition of a commonly used, model polyethylene (PE; weight average molecular weight (Mw) [~]4000 g/mol). We leveraged genome-resolved metatranscriptomics to identify active population affiliated with Acinetobacter guillouiae and Pseudomonas sp., showing a suite of upregulated genes (including those encoding alkane 1-monooxygenases, flavin-containing monooxygenases FMOs, cytochrome P450 monooxygenases) with functions compatible with degradation of oxidized products as well as medium- and long-chain hydrocarbons. Strikingly, spectroscopic, spectrometric and chromatographic analyses revealed the unexpected presence of medium- and long-chain alkanes and 2-ketones in the model PE substrate, preventing the erroneous conclusion that the community was interacting with the polymeric component. Consistently, only alkanes and 2-ketones with chain length of 10-35 were selectively degraded by an A. guillouiae isolate, as confirmed by proteomics analyses and substrate characterization following bacterial growth. Besides extending the knowledge on the enzymatic basis for degradation of PE-derivatives in soil-associated microbial systems, our results provide an advanced compositional characterization of a widely used model "PE" material, while offering valuable insight to support future studies aimed at unequivocally identifying organisms and their enzymes implicated in PE transformation.

microbiology↗

bioRxiv2025

Whole genome assembly and annotation of the Bumblebee Wax Moth, Aphomia sociella

The bumble bee wax moth, Apshomia sociella, is an important lepidopteran pest impacting bee colonies essential for pollination and apiculture. Despite its relevance, sequence efforts aimed at understanding the genetic makeup of this species have not yet been undertaken. In this work, we successfully achieved a high-quality de novo genome assembly of A. sociella and comprehensive gene annotations generated from long-read DNA and RNA sequencing with Oxford Nanopore technology. The haploid assembly includes 347 contigs, with an N50 of 4.96 Mb, and contains 27 242 protein-coding genes. Benchmarking Universal Single Copy Orthologs (BUSCO) analyses indicates that the assembly has a high level of completeness (98.3%) and low level of fragmentation (0.6%) and duplication (3.9%). Phylogenomic analyses with other members of the Lepidoptera order placed A. sociella in the same clade as Corcyra cephalonica and indicates close evolutionary relationships with the other two species in the subfamily Galleriinae, namely Achroia grisella and Galleria mellonella. This new high-quality genome assembly represents a valuable resource for investigating the genomic basis of ecological specialization of this species and offers critical support for research aimed at developing sustainable and effective pest management strategies.

genomics↗