Biology subjects

van Noort, V.

Publications and source records attributed to van Noort, V..

16 recordsLinked to original sources

bioRxiv2026

Genomic Potential vs. Pathogenic Reality: Functional Virulence Variation in Pseudomonas aeruginosa

Despite the rapid expansion of bacterial genome sequencing, predicting pathogen virulence from genomic information remains a major challenge. To study this association, we integrate comparative genomics, functional phenotyping, host-pathogen interaction assays, and infection outcomes across a diverse collection of 28 Pseudomonas aeruginosa isolates, representing clinically relevant diversity in serotype, type IV pilus group, and flagellar type. While virulence-associated systems were broadly retained across the strain collection, isolates displayed substantial variation in phenotypic behavior and pathogenicity. Genotypic classifications based on pilus, flagellar, siderophore, or secretion system characteristics were poor predictors of virulence-associated phenotypes. Pathogenicity in a Galleria mellonella model varied markedly among strains and was most strongly associated with surface-associated motility, whereas other virulence traits and quorum-sensing genotypes showed limited predictive value. In a three-dimensional lung epithelial cell model, inflammatory responses were negatively correlated with activity of the type III secretion system effector ExoS, suggesting a role in modulation of host immune signaling. Together, these findings demonstrate that virulence emerges from functional deployment of conserved virulence repertoires, rather than their mere presence. By linking genomic diversity to phenotypic expression, pathogenicity, and host responses within a single strain collection, this study highlights fundamental limitations of gene-content-based virulence prediction and underscores the importance of integrating genomic and functional data to better understand P. aeruginosa virulence.

microbiology↗

bioRxiv2026

AdventML: Advanced Enzyme Temperature Prediction with Transformer-Based Embeddings and Resampling Strategies

Accurate prediction of enzymes optimal catalytic temperature (Topt) is crucial in biotechnology, as enzymes with extreme Topt values are highly desirable for reactions at extreme temperatures and for their general stability. However, experimental determination of Topt is costly, labor-intensive, and time-consuming. Meanwhile, existing computational methods suffer from small and imbalanced datasets, subop-timal predictions at extreme temperatures, and insufficient validation. In this study, we address these challenges by expanding the Topt dataset and validating on an independent test set based on sequence similarity. We further tackle these limitations by comparing multiple resampling techniques to improve predictions at extremes and by considering diverse protein rep-resentations and multiple machine learning architectures. Overall, the best performing models reached R2 {approx} 0.64 with MAE {approx} 7-8 {degrees}C, while extreme resampling improved tail performance (reducing tail MAE by up to ~1.8 {degrees}C). Notably, our models show improved performance over state-of-the-art prediction models. We also demonstrate that accurate prediction of Topt is achievable even in the absence of organ-ism growth temperature (OGT). Our Topt prediction models are made freely available as AdventML on GitHub.

bioinformatics↗

bioRxiv2026

Evolution of the Cytochrome P450 Family 4 (CYP4) Subfamilies in Birds

Cytochrome P450 (CYP) genes form a large and functionally diverse superfamily of heme-thiolate monooxygenases that catalyse the oxidation of endogenous and exogenous compounds. Within this superfamily, CYP4 enzymes primarily act on fatty acids, substrates central to energy metabolism. Sustained flight and long-distance migration in birds rely on efficient use of fatty acids, making CYP4 a pertinent system for examining how lipid-associated functions may vary across avian lineages. Across Aves, species occupy diverse ecological niches and display substantial variation in metabolic demands. Here, we characterised CYP4 evolution across birds using 363 avian whole genomes, which cover over 90% of bird families, to investigate how gene variation relates to differences in ecological traits and metabolic strategies. Using this extensive genomic dataset, we identified 4 CYP4 subfamilies and analysed their patterns of sequence evolution. The analyses revealed conserved elements of the avian CYP4 repertoire alongside lineage-specific variation. Several amino-acid positions under positive selection were located within substrate recognition sites (SRS), regions that influence substrate binding and catalytic properties. Changes at these positions may reflect shifts in enzymatic function associated with differences in ecological or physiological traits among species. Overall, the results highlight SRS-associated variation within CYP4 that may reflect adaptive responses to environmental change. These findings advance understanding of how lipid-associated metabolic pathways have been shaped during avian diversification and provide insight into the evolutionary history of a CYP family linked to metabolic adaptation in birds.

evolutionary biology↗

bioRxiv2025

Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins

Phages, the viruses of bacteria, harbor an incredibly diverse repertoire of proteins capable of manipulating their bacterial hosts, inspiring many medical and biotechnological applications. However, to date, only a limited subset of that repertoire can be exploited, due to the difficulties in functionally elucidating these proteins. In this study, we investigated several structure-informed approaches to annotate hypothetical proteins from Pseudomonas infecting phages. We curated a representative dataset of over 10,000 proteins derived from NCBI, for which we predicted protein structures with ColabFold and assessed structural similarity via FoldSeek against the PDB, AlphaFold, and Phold databases. We evaluated multiple annotation strategies, including sequence-based (Pharokka), and structure-based (FoldSeek, Phold) methods. Our results show that up to 43 % of truly unannotated proteins can be functionally annotated when combining structure-informed approaches with UniProt-derived annotations. We highlight the complementarity of different databases and the importance of annotation quality filtering. This work provides a valuable resource of predicted structures and annotations, and offers insights into optimizing structure-based annotation pipelines for viral proteins, paving the way for deeper exploration of phage biology and its applications.

bioinformatics↗

bioRxiv2025

Machine learning for optimal growth temperature prediction of prokaryotes using amino acid descriptors

MotivationThe optimal growth temperature (OGT) of organisms is valuable in bioprospecting enzymes that work under extreme conditions. Existing OGT prediction models achieve high accuracy, but mainly capture trends of overrepresented groups in the training set including organisms that thrive at moderate temperatures and those from well-described taxa. ResultsIn this study, we incorporated weighted scoring and phylogenetic splits to improve the generalizability of the prediction models. We first built a new growth temperature dataset comprising more than 21,000 species distributed over all three domains of life, with special attention to include OGT and extreme temperature data. We then trained machine learning models on the OGT data of 6,401 prokaryotes using proteome-averaged amino acid descriptors. The best-performing model was the multilayer perceptron with a cross-validated RMSE of 5.07{degrees}C ({+/-} 0.24) and an R2 of 0.89 ({+/-} 0.04). The most important proteome features were related to backbone flexibility, charged residues, as well as surface accessibility. Availability and ImplementationThe MLP model is integrated in the command line tool OGTFinder and available under MIT license at: https://github.com/SC-Git1/OGTFinder.

microbiology↗

bioRxiv2023

Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa

The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14-1, YuA, PAK_P3 and giant phage phiKZ during early, middle and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including non-coding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.

microbiology↗

bioRxiv2022

The paradoxical relationship between CRISPR-Cas and phage susceptibility in Pseudomonas aeruginosa

CRISPR-Cas systems are part of the pan-immune system of Pseudomonas aeruginosa and have been shown to limit horizontal gene transfers in that species. Indeed, isolates equipped with these systems tend to have smaller genomes and CRISPR spacers targeting integrative conjugative elements, phages, and plasmids. In this work, we investigate the genomic effects and phenotypic consequences of CRISPR-Cas systems in P. aeruginosa. First, we establish that the population structure is a confounding factor of the relation between genome sizes and the presence of CRISPR-Cas systems in P. aeruginosa as isolates from group II are, on average, 200 kbp larger than those from group I, and have a lower likelihood of possessing CRISPR-Cas systems. Second, we show that the impact on the genome size of CRISPR deactivation by anti-CRISPR proteins differs between the various CRISPR-Cas types found in this species (I-C, I-E, and I-F). Finally, we highlight a paradoxical, positive correlation between the presence of CRISPR-Cas systems and the chances of the host being infected by a set of distinct, strictly virulent Pseudomonas phages. We propose that this increased phage susceptibility in the presence of CRISPR-Cas is linked to a depletion of other accessory defense system genes in isolates with CRISPR-Cas systems. Note: This manuscript was published as a chapter in the doctoral dissertation of Cedric Lood [72]

microbiology↗

bioRxiv2022

Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes

The Aryl hydrocarbon receptor is an ancient transcriptional factor originally discovered as a sensor of dioxin. In addition to its function as receptor of environmental toxins, it plays an important role in development. Although a significant amount of research has been carried out to understand AHR signal transduction pathway and its involvement in species susceptibility to environmental toxins, none of them to date has comprehensively studied its evolutionary origins. Studying evolutionary origins of molecules can inform ancestral relationships of genes. Vertebrate genome has been shaped by two rounds of whole-genome duplications at the base of vertebrate evolution approximately 600 million years ago (Mya), followed by lineage specific gene losses, which often complicate assignment of functional homology. It is crucial to understand evolutionary origins of this transcription factor and its partners, in order to distinguish orthologs from ancient non-orthologous homologs. In this study, we have investigated evolutionary origins of proteins involved in the AHR pathway. Our results provide evidence of gene loss and duplications, crucial for understanding functional connectivity of human and model species. Multiple studies have shown that 2R-ohnologs (genes and proteins that have survived from the 2R-WGD) are enriched in signaling components relevant to developmental disorders and cancer. Our findings provide a link between AHR pathways evolutionary trajectory and its possible mechanistic involvement in pathogenesis.

bioinformatics↗

bioRxiv2021

Analyses of the complete genome sequence of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of (un)stable plasmids.

Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its transformation product, the recalcitrant groundwater micropollutant, 2,6-dichlorobenzamide (BAM) as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, resulting in the use of additional treatment in drinking water treatment plants (DWTPs) or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. Combining Illumina and Nanopore sequencing, we here present the complete genome of MSH1, which was determined independently in two different laboratories. Unexpectedly, divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism pBAM1 (41 kb) and pBAM2 (54 kb), we observe that the genome of MSH1 contains two megaplasmids pUSP1 (367 kb) and pUSP2 (366 kb) and three smaller plasmids pUSP3 (97 kb), pUSP4 (64 kb), and pUSP5 (32 kb). The MSH1 substrain from KU Leuven showed a reduced genome lacking plasmids pUSP2 and the three smaller plasmids and was designated substrain MK1, whereas the variant with all plasmids was designated as substrain DK1. Results of a plasmid stability experiment, indicate that strain MSH1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Based on phylogenetic analyses, strain MSH1 is reassigned as Aminobacter niigataensis MSH1. ImportanceThe complete genomes of the two MSH1 substrains, DK1 and MK1, provide further insight into this already well-studied organism with bioremediation potential. The varying plasmid contents in the two substrains suggest that some of the plasmids are unstable, although this is not supported by the herein described plasmid stability experiment. Instead, results suggest that MSH1 is polyploid with respect to its chromosome, at least under some growth conditions. As the essential BAM-degradation genes are found on some of these plasmids, stable inheritance is essential for continuous removal of BAM. Finally, Aminobacter sp. MSH1 is reassigned as Aminobacter niigataensis MSH1, based on phylogenetic evidence.

microbiology↗

bioRxiv2020

The fully resolved genome of Bacillus thuringiensis HER1410 reveals a cry-containing chromosome, two megaplasmids & an integrative plasmidial prophage

Bacillus thuringiensis is the most used biopesticide in agriculture. Its entomopathogenic capacity stems from the possession of plasmid-borne insecticidal crystal genes (cry), traditionally used as discriminant taxonomic feature for that species. As such, crystal and plasmid identification are key to the characterization of this species. To date, about 600 B. thuringiensis genomes have been reported, but less than 5% have been resolved, while the other draft genomes are incomplete, precluding plasmid delineation. Here we present the complete genome of Bacillus thuringiensis HER1410, a strain closely related to B. thuringiensis entomocidus and a known host for a variety of Bacillus phages. The combination of short and long-reads techniques allowed fully resolving the genome and delineation of three plasmids. This enabled the accurate detection of an unusual location of a unique cry gene, cry1Ba4, located in a genomic island near the chromosome replication origin. Two megaplasmids, pLUSID1 and pLUSID2 could be delineated: pLUSID1 (368kb), a likely conjugative plasmid involved in virulence, and pLUSID2 potentially related to the sporulation process. A smaller plasmidial prophage pLUSID3, with a dual lifestyle whose integration within the chromosome, causes the disruption of a flagellar key component. Finally, phylogenetic analysis located this strain within a clade comprising members from the B. thuringiensis serovar thuringiensis and other serovars and with B.cereus s. s. This highlights the intermingled taxonomy of B. cereus sensu lato group, where genomics alone does not support the present taxonomy between B. cereus s. s. and B. thuringiensis as species designation currently relies solely on the presence of entomocidal genes. ImportanceBacillus cereus group species have been extensively studied due to their economical and clinical relevance. This importance originally set the basis for B. cereus group members classification which are commonly based on phenotypical criteria. Sequencing era has shed light about genomic characterization of these species, showing their chromosomal genomic similarity and highlighting the role of mobile genetic elements, especially megaplasmids, in the classification and characterization of this group. However, only the 5% of the sequenced B. thuringiensis genomes have been fully resolved. Thus, here we addressed efficiently the study B. thuringiensis HER1410 genomic features by the use of a combination of short and long-reads sequencing. This methodology resulted in the high-quality assembly, which led to the identification of an uncommon location of a cry gene close to the chromosomal origin, as well as three fully resolved extrachromosomal elements, two megaplasmids and an integrative plasmidial prophage.

microbiology↗

bioRxiv2020

A suppressor of axillary meristem maturation promotes longevity in flowering plants

Post embryonic development and growth of flowering plants are for a large part determined by the activity and maturation state of stem cell niches formed in the axils of leaves, the so-called axillary meristems (AMs)1,2. Here we identify a new role for the Arabidopsis AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15) gene as a suppressor of AM maturation. Loss of AHL15 function accelerates AM maturation, whereas ectopic expression of AHL15 suppresses AM maturation and promotes longevity in Arabidopsis and tobacco. Together our results indicate that AHL15 expression acts as a key molecular switch, directly downstream of flowering genes (SOC1, FUL) and upstream of GA biosynthesis, in extending the plants lifespan by suppressing AM maturation.

plant biology↗

bioRxiv2019

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Pseudomonas virus vB_PaeM_PA5oct is a compelling model phage to investigate phage-bacteria interactions and is a potent candidate for phage therapy. Combining hybrid genome sequencing, RNA-Seq, and mass spectrometry of virion-associated proteins allowed us to accurately assemble and annotate PA5octs 286,783 bp genome. It encodes 461 coding regions, of which 93 were identified as virion-associated proteins using ESI-MS/MS. RNA-seq revealed twelve tRNA genes, four ncRNA regions, and a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. Although PA5oct is not organized into strictly contiguous regions of temporal transcription, defined genomic regions are expressed in early, middle, and late phases of infection. Interestingly, we observed distinct regions showing limited transcription activity throughout the infection cycle. The infection of Pseudomonas aeruginosa by PA5oct triggers the upregulation of bacterial operons related to NAD biosynthesis, Psl exopolysaccharide, and periplasmic nitrate reductase production and downregulates Type IV pili gene products, suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position this isolate amongst other phages using a protein-sharing network. This study expands our understanding of the molecular diversity of jumbo viruses and opens new questions towards cellular regulation and phage-encoded hijacking mechanisms.

molecular biology↗

bioRxiv2019

Megaplasmids on the rise: combining sequencing approaches to fully resolve a carbapenemase-encoding plasmid in a proposed novel Pseudomonas species

Horizontal transfer of plasmids plays a pivotal role in the dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Sequencing of plasmids is thus paramount for the success of accurate epidemiological tracking strategies in the hospital setting and routine surveillance. Here, we combine Nanopore and Illumina sequencing to fully assemble a carbapenemase-encoding megaplasmid carried by a clinical isolate belonging to a putative novel Pseudomonas species. FFUP_PS_41 has a multidrug resistance phenotype and was initially identified as Pseudomonas putida, but an average nucleotide identity below the cut-off for species delineation suggests a new species related to the P. putida phylogenetic group. FFUP_PS_41 harbors a 498,516-bp untypable megaplasmid (pJBCL41) with low similarity compared with publicly available plasmids. pJBCL41 contains a full set of genes for self-transmission and genes predicted to be responsible for plasmid replication, partitioning, maintenance and heavy metal resistance. pJBCL41 carries a class 1 integron with the |aacA7|blaVIM-2|aacA4| cassette array (In103) located within a defective Tn402-like transposon that forms part of a 50,273-bp mosaic region bound by 38-bp inverted repeats typical of the Tn3 family and flanked by 5-bp direct repeats. This region is composed of different elements, including additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach resulted in contiguous assemblies and allowed us to fully resolve a carbapenemase-encoding megaplasmid from Pseudomonas spp. The identification of novel megaplasmids will shed a new light on the evolutionary effects of gene transfer and the selective forces driving AR.

microbiology↗

bioRxiv2019

A genome-based species taxonomy of the Lactobacillus Genus Complex

BackgroundThere are over 200 published species within the Lactobacillus Genus Complex (LGC), the majority of which have sequenced type strain genomes available. Although gold standard, genome-based species delimitation cutoffs are accepted by the community, they are seldom checked against currently available genome data. In addition, there are many species-level misclassification issues within the LGC. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available, decent-quality genomes and using a 94% core nucleotide identity threshold. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains in our dataset and (ii) performing comparisons based on 16S rRNA sequence identity against type strains. ResultsWe found that genomes within the LGC could be divided into 239 clusters (de novo species) that were discontinuous and exclusive. Comparison of these de novo species to published species lead to the identification of ten sets of published species that can be merged and one species that can be split. Further, we found at least eight genome clusters that constitute new species. Finally, we were able to accurately classify 98 unclassified genomes and reclassify 74 wrongly classified genomes. ConclusionsThe current state of LGC species taxonomy is largely consistent with genome data, but there are some inconsistencies as well as genome misclassifications. These inconsistencies should be resolved to evolve towards a meaningful taxonomy where species have a consistent size in terms of sequence divergence.

bioinformatics↗

bioRxiv2018

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana

Several recent studies indicate that small Open Reading Frames (sORFs) embedded within multiple eukaryotic non-coding RNAs can be translated into bioactive peptides of up to 100 amino acids in size. However, the functional roles of the 607 Stress Induced Peptides (SIPs) previously identified from 189 Transcriptionally Active Regions (TARs) in Arabidopsis thaliana remain unclear. To provide a starting point for function annotation of these peptides, we performed a large-scale prediction of peptide binding sites on protein surfaces using and coarse-grained peptide docking. The docked models were subjected to further atomistic refinement and binding energy calculations. A total of 530 peptide-protein pairs were successfully docked. In cases where a peptide encoded by a TAR is predicted to bind at a known ligand or cofactor-binding site within the protein, it can be assumed that the peptide modulates the ligand or cofactor-binding. Moreover, we predict that several peptides bind at protein-protein interfaces, which could therefore regulate the formation of the respective complexes. Protein-peptide binding analysis further revealed that peptides employ both their backbone and side chain atoms when binding to the protein, forming predominantly hydrophobic interactions and hydrogen bonds. In this study, we have generated novel predictions on the potential protein-peptide interactions in A. thaliana, which will help in further experimental validation.\n\nAuthor summaryDue to their small size, short peptides are difficult to find and have been ignored in genome annotations. Only recently, we have realized that these short peptides of less than 100 amino acids may actually play an important role in the cell. Currently, there are no high-throughput methods to find out what the functions of these peptides are in contrast with efforts that exist for normalproteins. In this work, we try to fill this gap by predicting with which larger proteins, the short peptides might interact to exert their function. We find that many peptides bind to pockets where normally other proteins or molecules bind. We thus think that these peptides that are induced by stress, may regulate protein-protein and protein-molecule binding. We make this information available through our database ARA-PEPs so that individual predictions can be followed up.

bioinformatics↗

bioRxiv2018

Gender balance in time-keeping at life science conferences

Scientific conferences are biased against women when selecting speakers, but recent studies showed a positive trend where the ratio of invited female speakers had increased. We have recorded speaking times at 11 different conferences during 2016-2017 to analyze which factors influenced a speakers time keeping. Men and women went over time 47% and 41% of the talks, respectively. In a regression analysis, it was found that the most important factors that influences how long a presenter spoke was 1) their allocated time, 2) their career stage and 3) the level of time keeping enforcement. It was also found that gender and the size of the conference contributed significantly towards the speakers timing. Male speakers exceeded their allocated time more frequently than female speakers, especially at large conferences (60% vs 49%). Since conferences are an important arena for science dissemination this might have a negative impact on female scientists careers.

scientific communication and education↗