Biology subjects

Andersen, T.

Publications and source records attributed to Andersen, T..

8 recordsLinked to original sources

bioRxiv2025

Entry Steps in the Biosynthetic Pathway to DiterpenoidAlkaloids in Delphinium grandiflorum and Aconitum plicatum

Both the terpenoid and alkaloid classes of specialized metabolites have received considerable attention for their wide range of practical applications, however, few examples have been identified of these classes intersecting. The diterpenoid alkaloids are one such example of nitrogen-containing terpenoids which are found throughout many independent plant lineages, but primarily within the Aconitum (Wolfs-Bane) and Delphinium (Larkspur) genera. While there is considerable interest in these compounds for their wide range of bioactivities, their structural complexity often precludes their production through chemical synthesis, and little progress has been made towards elucidation of their biosynthetic pathways. Here, we employ a comparative transcriptomics approach to identify six enzymatic steps in the biosynthesis of atisinium, conserved across both Delphinium grandiflorum and Aconitum plicatum. Key to this pathway is a reductase which selectively incorporates ethanolamine over ethylamine into the diterpenoid scaffold. While the majority of diterpenoid alkaloids contain an ethylamine moiety, we demonstrate through isotope labeling in Aconitum callus cultures and a computational metabolomics approach that ethanolamine is, unintuitively, the preferred source of nitrogen for these metabolites. Identification of these enzymes and production of a key intermediate in a heterologous host paves the way for biosynthetic production of this group of metabolites with promise for medicinal applications.

biochemistry↗

bioRxiv2024

CYP76BK1 orthologs catalyze furan and lactone ring formation in clerodane diterpenoids across the mint family

The Lamiaceae (mint family) is the largest known source of furanoclerodanes, a subset of clerodane diterpenoids with broad bioactivities including insect antifeedant properties. The Ajugoideae subfamily, in particular, accumulates significant numbers of structurally related furanoclerodanes. The biosynthetic capacity for formation of these diterpenoids is retained across most Lamiaceae subfamilies, including the early-diverging Callicarpoideae which forms a sister clade to the rest of Lamiaceae. VacCYP76BK1, a cytochrome P450 monooxygenase from Vitex agnus-castus, was previously found to catalyze the formation of the proposed precursor to furan and lactone-containing labdane diterpenoids. Through transcriptome-guided pathway exploration, we identified orthologs of VacCYP76BK1 in Ajuga reptans and Callicarpa americana. Functional characterization demonstrated that both could catalyze the oxidative cyclization of clerodane backbones to yield a furan ring. Subsequent investigation revealed a total of ten CYP76BK1 orthologs across six Lamiaceae subfamilies. Through analysis of available chromosome-scale genomes, we identified four CYP76BK1 members as syntelogs within a conserved syntenic block across divergent subfamilies. This suggests an evolutionary lineage that predates the speciation of the Lamiaceae. Functional characterization of the CYP76BK1 orthologs affirmed conservation of function, as all catalyzed furan ring formation. Additionally, some orthologs yielded two novel lactone ring moieties. The presence of the CYP76BK1 orthologs across Lamiaceae subfamilies closely overlaps with the distribution of reported furanoclerodanes. Together, the activities and distribution of the CYP76BK1 orthologs identified here support their central role in furanoclerodane biosynthesis within the Lamiaceae family. Our findings lay the groundwork for biotechnological applications to harness the economic potential of this promising class of compounds. Significance StatementThe discovery and functional characterization of CYP76BK1 orthologs across diverse Lamiaceae subfamilies revealed novel chemistry and their central role in furanoclerodane biosynthesis, providing insights into the metabolic landscape and dynamic evolution of this plant family over approximately 50 million years. These findings pave the way for targeted biosynthetic engineering efforts and the sustainable production of furanoclerodane compounds, offering promising prospects for agricultural and pharmaceutical applications.

plant biology↗

bioRxiv2023

A method for storing information in DNA with improved dropout tolerance

Storing information in synthetic DNA oligomers is attractive for archival purposes due to the favorable physical density, stability, and energy efficiency of this storage medium. However, issues with this medium sometimes cause dropout (i.e., loss of oligomers) which may prevent the recovery of stored information. Here, an improved information storage method derived from the existing "DNA Fountain" method is reported. In this work we have developed and experimentally tested a robust algorithm to write digital data in pools of DNA strands by applying a rateless erasure code (i.e., fountain code), a Reed Solomon code, and an oligomer mapping code. Our new method includes changes to the fountain code, the oligomer mapping code, and the encoding and decoding processes. We have tested and benchmarked our algorithm vs similar algorithms and found that our method increases robustness to dropout, decreases encoding time, and decreases decoding time. The new method was validated in-vitro by successfully storing and recovering 105,360 bits of information. The advantages of the new method make it more appropriate for applications where information recovery is critical, where substantial sequence loss is expected, and/or where computational resources are limited. Furthermore, the inclusion of the novel oligomer mapping code enabled us to mitigate errors by restricting sequences of repeated bases and enhance security by eliminating start/stop codons, thus minimizing the risk of interaction with living cells.

bioinformatics↗

bioRxiv2022

The metabolic influence of the core ciliate Entodinium caudatum within the rumen microbiome

Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.

microbiology↗

bioRxiv2022

Cell size and actin architecture determine force generation in optogenetically activated adherent cells

Adherent cells use actomyosin contractility to generate mechanical force and to sense the physical properties of their environment, with dramatic consequences for migration, division, differentiation and fate. However, the organization of the actomyosin system within cells is highly variable, with its assembly and function being controlled by small GTPases from the Rho-family. How activation of these regulators translates into cell-scale force generation and the corresponding sensing capabilities in the context of different physical environments is not understood. Here we probe this relationship combining recent advances in non-neuronal optogenetics with micropatterning and traction force microscopy on soft elastic substrates. We find that after whole-cell RhoA-activation by the CRY2/CIBN optogenetic system with a short pulse of 100 milliseconds, single cells contract before returning to their original tension setpoint with near perfect precision on a time scale of several minutes. To decouple the biochemical and mechanical elements of this response, we introduce a mathematical model that is parametrized by fits to the dynamics of the substrate deformation energy. We find that the RhoA-response builds up quickly on a time scale of 20 seconds, but decays slowly on a time scale of 50 seconds. The larger the cells and the more polarized their actin cytoskeleton, the more substrate deformation energy is generated. RhoA-activation starts to saturate if optogenetic pulse length exceeds 50 milliseconds, revealing the intrinsic limits of biochemical activation. Together our results suggest that adherent cells establish tensional homeostasis by the RhoA-system, but that the setpoint and the dynamics around it are strongly determined by cell size and the architecture of the actin cytoskeleton, which both are controlled by the extracellular environment.

biophysics↗

bioRxiv2021

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

Understanding how periodical disturbances affect the community assembly processes is vital for predicting temporal dynamics in microbial communities. The effect of dilutions as disturbances are poorly understood. We used a marine bacterial community to investigate the effect of disturbance (+/-) and carrying capacity (high/low) over 50 days in a dispersal-limited 2x2 factorial crossover study in triplicates. The communitys disturbance regime was crossed halfway. We modelled the rate of change in community composition between replicates and used this rate to quantify selection and ecological drift. The disturbed communities increased in Bray-Curtis similarity with 0.011{+/-}0.0045 (Period 1) and 0.0092{+/-}0.0080 day-1 (Period 2), indicating that selection dominated community assembly. The undisturbed communities decreased in similarity at a rate of -0.015{+/-}0.0038 day-1 in Period 1 and were stable in Period 2 at 0.00050{+/-}0.0040 day-1, suggesting drift structured community assembly. Interestingly, carrying capacity had minor effects on community dynamics. This study is the first to show that stochastic effects are suppressed by periodical disturbances resulting in exponential growth periods due to density-independent biomass loss and resource input. The increased contribution of selection as a response to disturbances implies that ecosystem prediction is achievable.

ecology↗

bioRxiv2021

Neural networks and extreme gradient boosting predict multiple thresholds and trajectories of microbial biodiversity responses due to browning

Ecological association studies often assume monotonicity such as between biodiversity and environmental properties although there is growing evidence that non-monotonic relations dominate in nature. Here we apply machine learning algorithms to reveal the non-monotonic association between microbial diversity and an anthropogenic induced large scale change, the browning of freshwaters, along a longitudinal gradient covering 70 boreal lakes in Scandinavia. Measures of bacterial richness and evenness (alpha diversity) showed non-monotonic trends in relation to environmental gradients, peaking at intermediate levels of browning. Depending on the statistical methods, variables indicative for browning could explain 5% of the variance in bacterial community composition (beta diversity) when applying standard methods assuming monotonic relations and up to 45 % with machine learning methods (i.e. extreme gradient boosting and feed-forward neural networks) taking non-monotonicity into account. This non-monotonicity observed at the community level was explained by the complex interchangeable nature of individual taxa responses as shown by a high degree of non-monotonic responses of individual bacterial sequence variants to browning. Furthermore, the non-monotonic models provide the position of thresholds and predict alternative bacterial diversity trajectories in boreal freshwater as a result of ongoing climate and land use changes, which in turn will affect entire ecosystem metabolism and likely greenhouse gas production.

microbiology↗

bioRxiv2020

Evaluating geographic variation within molecular operational taxonomic units (OTUs) using network analyses in Scandinavian lakes

Operational taxonomic units (OTUs) are usually treated as if they are internally uniform in environmental metabarcoding studies of microbial and macrobial eukaryotes, even when the OTUs are being used to infer biogeographic patterns. The OTUs constructed by the program Swarm have underlying network topologies in which nodes represent amplicons and edges represent 1 nucleotide differences between nodes. Such networks can be exploited to search for biogeographic patterns within each OTU. To do this, here we used an available protistan metabarcoding dataset consisting of the hypervariable V4 region of the 18S rRNA locus amplified from 77 lakes collected across Norway and Sweden. The 82 most abundant and wide-spread OTUs constructed by Swarm were evaluated using shortest path, assortativity, and geographical analyses. We found that while pairs of amplicons from the same lake were usually connected directly to each other within the OTUs, these pairs of amplicons from the same lake did not form assortative clusters within the OTUs, and amplicons were not more connected with other amplicons occurring in neighboring lakes than expected by chance. This new approach to looking at within-OTU is applicable to other metabarcoding datasets and we provide code to perform these analyses.

microbiology↗