Biology subjects

Volkers, R. J. M.

Publications and source records attributed to Volkers, R. J. M..

4 recordsLinked to original sources

bioRxiv2022

Identification of Aspergillus niger aquaporins involved in hydrogen peroxide signaling

Aspergillus niger is a robust microbial cell factory for organic acids production. However, the regulation of many industrially important pathways is still poorly understood. Recently the regulation of glucose oxidase (GOx) expression system involved in the biosynthesis of gluconic acid has been uncovered. Hydrogen peroxide, a by-product of the enzymatic conversion of glucose to gluconate, has a pivotal role as a signaling molecule in the induction of this system. In this study, facilitated diffusion of hydrogen peroxide via aquaporin water channels (AQPs) was studied. AQPs are transmembrane proteins of the major intrinsic proteins (MIPs) superfamily. In addition to water and glycerol, they may also transport small solutes such as hydrogen peroxide. Accordingly, the genome sequence of A. niger N402 was screened for putative AQPs. Seven were found which could be classified in three main groups. Their ability to facilitate diffusion of hydrogen peroxide was identified using yeast phenotypic growth assays and by studying AQP gene knock-outs in A. niger. Complementing from both yeast and A. niger experiments, the X-intrinsic protein AQPF plays apparent roles in facilitating hydrogen peroxide transport across cellular membrane. IMPORTANCEAquaporins (AQP) are integral membrane proteins that facilitate transfer of water, small solutes and hydrogen peroxide across the plasma membrane. As they have conserved structural features, it is not difficult to detect their presence in fungal genomes. Their specific roles in fungi are however less understood. Previously we have elucidated the role of the hydrogen peroxide as a second messenger in the induction and regulation of the expression of glucose oxidase involved in the extracellular conversion of glucose in gluconate (1). Here we identified the involvement of AQPF, a member of the X-intrinsic protein class in facilitating transport of the hydrogen peroxide signal across the cell membrane.

molecular biology↗

bioRxiv2020

Punctuated loci on chromosome IV determine natural variation in Orsay virus susceptibility of Caenorhabditis elegans strains Bristol N2 and Hawaiian CB4856

Host-pathogen interactions play a major role in evolutionary selection and shape natural genetic variation. The genetically distinct Caenorhabditis elegans strains, Bristol N2 and Hawaiian CB4856, are differentially susceptible to the Orsay virus (OrV). Here we report the dissection of the genetic architecture of susceptibility to OrV infection. We compare OrV infection in the relatively resistant wild-type CB4856 strain to the more susceptible canonical N2 strain. To gain insight into the genetic architecture of viral susceptibility, 52 fully sequenced recombinant inbred lines (CB4856 x N2 RILs) were exposed to OrV. This led to the identification of two loci on chromosome IV associated with OrV resistance. To verify the two loci and gain additional insight into the genetic architecture controlling virus infection, introgression lines (ILs) that together cover chromosome IV, were exposed to OrV. Of the 27 ILs used, 17 had an CB4856 introgression in an N2 background and 10 had an N2 introgression in a CB4856 background. Infection of the ILs confirmed and fine-mapped the locus underlying variation in OrV susceptibility and we found that a single nucleotide polymorphism in cul-6 contributes to the difference in OrV susceptibility between N2 and CB4856. An allele swap experiment showed the strain CB4856 became more susceptible by having an N2 cul-6 allele, although having the CB4856 cul-6 allele did not increase resistance in N2. Additionally, we found that multiple strains with non-overlapping introgressions showed a distinct infection phenotype from the parental strain, indicating that there are punctuated locations on chromosome IV determining OrV susceptibility. Thus, our findings reveal the genetic complexity of OrV susceptibility in C. elegans and suggest that viral susceptibility is governed by multiple genes.

genetics↗

bioRxiv2019

Dissecting the eQTL micro-architecture in Caenorhabditis elegans

The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on local and distant regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by mapping eQTL in N2 x CB4856 C. elegans RIL populations across three different environments (control, heat-stress, and recovery). To test for independent replication of the RIL eQTL, we used introgression lines (ILs). Both populations indicate that the overall heritability, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the local- and 40% of the distant-eQTL using the ILs. Simulation models revealed that additive effects explain up to 60-93% of RIL/IL heritability across environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for local vs. distant eQTL and that the environment affects the eQTL micro-architecture.

genetics↗

bioRxiv2018

A multi-parent recombinant inbred line population of Caenorhabditis elegans enhances mapping resolution and identification of novel QTLs for complex life-history traits

Local populations of the bacterivorous nematode Caenorhabditis elegans can be genetically almost as diverse as global populations. To investigate the effect of local genetic variation on heritable traits, we developed a new recombinant inbred line (RIL) population derived from four wild isolates. The wild isolates were collected from two closely located sites in France: Orsay and Santeuil. By crossing these four genetically diverse parental isolates a population of 200 RILs was constructed. RNA-seq was used to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the four genotypes with an average spacing of 11 kb, possibly doubling the mapping resolution relative to currently available RIL panels. The SNPs were used to construct a genetic map to facilitate QTL analysis. Life history traits, such as lifespan, stress resistance, developmental speed and population growth were measured in different environments. For most traits substantial variation was found, and multiple QTLs could be detected, including novel QTLs not found in previous QTL analysis, for example for lifespan or pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. Taken together, we show that RNA-seq can be used for genotyping, that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates permits analysis of local adaptation and life history trade-offs.

genetics↗