Biology subjects

Bervoets, I.

Publications and source records attributed to Bervoets, I..

4 recordsLinked to original sources

bioRxiv2025

Development and characterisation of pNarsenic: a naringenin-inducible biosensor for arsenic in Escherichia coli

Whole-cell biosensors detecting the heavy metal arsenic have been widely studied for their potential in environmental monitoring. And while inducible biosensors have been shown to be an effective tool to tune the operational range, a thoroughly characterised inducible biosensor is currently lacking. Here, we present an Escherichia coli biosensor for arsenic in which the transcription factor gene arsR is inducible by naringenin, a plant-derived secondary metabolite. Increasing naringenin concentrations reduced the basal output while increasing both the dynamic range and sensing threshold of the biosensor dose-response curves, but the operational ranges appeared constrained by a fixed upper limit. Comparison with a previously published phenomenological model revealed good overall agreement between experimental data and model predictions, except for the behaviour of the maximum output and threshold. This work expands the biosensor toolbox with a profoundly characterised arsenic biosensor and raises a potential practical limit to dose-response curve engineering by tuning transcription factor expression alone. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/678503v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@c15051org.highwire.dtl.DTLVardef@180214forg.highwire.dtl.DTLVardef@10afa84org.highwire.dtl.DTLVardef@1c51bba_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Transcriptional regulation of the type II fatty acid synthase complex in Rhodococcus opacus

Rhodococcus opacus is an oleaginous actinobacterium with considerable potential for lipid-based bioproduction, as well as for utilising a variety of carbon sources as substrates, including renewable, cost-effective resources. Although its capacity for triacylglycerol accumulation is well established, the regulatory logic that governs its fatty acid and mycolic acid biosynthesis is still poorly understood. Here, we investigated the transcriptional control of the type II fatty acid synthase (FASII) pathway in R. opacus PD630, revealing a regulatory architecture that is more complex than previously assumed. Differential gene expression analysis showed that environmental cues, including temperature, pH, carbon-to-nitrogen ratio and the presence of free fatty acids influence the FASII gene cluster expression in a non-uniform manner. This phenomenon suggests the presence of internal transcription start sites and modular regulation within the cluster. We identified three lipid-responsive transcription factors, MabRRO, FadR1RO and FadR2RO, that are all capable of binding the fasII promoter in vitro. DNA binding of FadR1RO and FadR2RO was disrupted by long-chain acyl-CoA molecules, indicating ligand-dependent control. Together, these findings reveal previously unrecognised layers of transcriptional regulation in the R. opacus FASII pathway and highlight both conserved and divergent regulatory features within the Mycobacteriales lineage. Featured Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/678588v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@456a6dorg.highwire.dtl.DTLVardef@14e3d1forg.highwire.dtl.DTLVardef@18ed368org.highwire.dtl.DTLVardef@1d979a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Effects of genomic location on ectopic integration and gene expression of a reporter gene cassette in Sulfolobus acidocaldarius

In eukaryotes and bacteria, it is well-established that the genomic location of ectopic gene integration influences the expression level due to replication-associated gene dosage effects as well as effects mediated by chromatin organization. In contrast, in archaea, the impact of genomic location on gene expression remained unexplored. Here, we investigated this impact in the model archaeon Sulfolobus acidocaldarius, a crenarchaeal species that has a chromatin architecture with mixed eukaryotic-like and bacterial-like features. We aimed to integrate a standardized {beta}-galactosidase (lacS) reporter cassette into diverse loci in the genome of S. acidocaldarius SK-1 for a comparative analysis. Nine integration mutant strains were successfully obtained, for which qRT-PCR analysis and lacS reporter gene assays revealed significant variation in transcriptional and translational expression of the reporter, respectively, demonstrating that genomic location strongly influences gene expression in S. acidocaldarius. However, variability in transcription levels and its regulation was shown to be primarily driven by transcriptional activity of neighboring genes, due to the high coding density in the S. acidocaldarius genome as well as a lack of insulator elements. Interestingly, translational activity exhibited a more apparent correlation with the distance to the closest origin of replication (R2 = 0.432) as compared to transcriptional activity (R2 = 0.026). In conclusion, this study not only provides insights into genome context effects, but also provides inspiration for the future design of genomic knock-in constructions in S. acidocaldarius.

microbiology↗

bioRxiv2024

Protein kinase Sut1 from the Crenarchaeon Sulfolobus acidocaldarius displays tyrosine phosphorylation activity

Protein phosphorylation is a key cellular signaling mechanism that exists in all life forms. Unlike Bacteria and Eukarya, in which protein phosphorylation has thoroughly been studied, post-translational modification by means of phosphorylation have only been limitedly explored in Archaea. A previous study of the phosphoproteome of the model Crenarchaeon Sulfolobus acidocaldarius revealed a widespread occurrence of protein phosphorylation, especially on tyrosine residues. Moreover, several (putative) transcription factors, including AbfR1 and FadR, were previously shown to be phosphorylated on tyrosine residues, a phenomenon that is directly linked to a phosphorylation-mediated regulation of these transcription factors. Despite this potentially important role for tyrosine phosphorylation in S. acidocaldarius, to our knowledge, a kinase capable of directly phosphorylating tyrosine residues has not yet been identified in this organism, neither in Archaea as a whole. Here, we identify and characterize a protein kinase in S. acidocaldarius, Sut1, which displays tyrosine phosphorylation activity in vitro and represents a novel protein kinase family that is widespread in different archaeal organisms.

microbiology↗