Biology subjects

Behrens, S.-E.

Publications and source records attributed to Behrens, S.-E..

4 recordsLinked to original sources

bioRxiv2026

SNPstar: A Web Server Linking Allelic Variation to Protein Structure and Function in Arabidopsis thaliana

Understanding how natural genetic variants affect protein structure and function is central to plant biology. The 1001 Genomes Project has catalogued millions of single nucleotide polymorphisms (SNPs) across more than a thousand Arabidopsis thaliana accessions, offering an unprecedented opportunity to relate sequence variation to three-dimensional protein structure and population context. Yet, realizing it requires tools that integrate these scales in one accessible framework. Here we present SNPstar, a web server that links allelic variation in A. thaliana to AlphaFold3-predicted structures through a gene-centric, interactive interface. SNPstar annotates each variant with descriptive features, thermodynamic stability estimates, protein domain context, and genome-wide association results, and computes haplotypes and proteotypes that group accessions by shared DNA or protein sequence. Researchers can characterize variants, visualize their structural context, map their geographic distribution, and prioritize accessions for experimental validation without local computational infrastructure. We demonstrate SNPstar with two case studies. The first recapitulates known loss-of-function variation in the cadmium transporter HMA3, validating that SNPstar prioritizes functionally consequential alleles. The second uses SNPstar-defined proteotypes to identify an N-terminal SNP combination in ARGONAUTE 2 that distinguishes accessions differing in in vitro siRNA-directed target cleavage, linking protein-coding variation to a measurable molecular phenotype. SNPstar thus helps translate natural variation into mechanistic insight.

plant biology↗

bioRxiv2025

A flexible Janus head: molecular determinants of a viral protein's RNAi suppressor and capsid forming activities

Viral suppressors of RNA silencing (RNAi) expressed by plant viruses, VSRs, are exceptional proteins. Although not conserved, even within virus families, most VSRs bind small interfering RNAs, siRNAs, thereby blocking antiviral RNAi. Turnip crinkle virus, a member of the Tombusviridae family, encodes a VSR, TCV P38, which also forms the viral capsid. Biochemical studies of the purified protein revealed that the TCV P38 VSR functions as a metastable dimer that binds double-stranded (ds) RNA with high affinity via an induced-fit mechanism of both binding partners. Consistent with its role as a VSR that interferes with antiviral RNAi at various stages, P38 distinguishes between siRNAs of different lengths. Consistent with its capsid-forming function, the protein binds longer dsRNAs cooperatively. Structural data obtained from an RNA-free capsid-like icosahedral crystal and modeling of Tombusviridae capsid proteins suggest that flexible interactions between the P (protruding)-domains of P38 are important determinants for forming both the VSR dimer and the capsid structure. Studies with protein mutants confirmed this and also revealed the central role of the S (shell)- and R (RNA-binding)-domains of TCV P38 in adaptive substrate binding. Our study provides comprehensive insights into the molecular and structural properties of a versatile viral "Janus head" protein. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/690650v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@185f6b1org.highwire.dtl.DTLVardef@6e773org.highwire.dtl.DTLVardef@1456981org.highwire.dtl.DTLVardef@11a63e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

A new level of RNA-based plant protection - dsRNAs designed from functionally characterized siRNAs highly effective against Cucumber Mosaic Virus

RNA-mediated crop protection increasingly becomes a viable alternative to agrochemicals that threaten biodiversity and human health. Pathogen-derived double-stranded dsRNAs are processed into small interfering RNAs (siRNAs), which can then induce silencing of target RNAs, e.g. viral genomes. However, with currently used dsRNAs, which largely consist of undefined regions of the target RNAs, silencing is often ineffective: processing generates siRNA pools that contain only a few functionally effective siRNAs (here called esiRNAs). Using a recently developed in vitro screen that reliably identifies esiRNAs from siRNA pools, we identified esiRNAs against Cucumber Mosaic Virus (CMV), a devastating plant pathogen. Topical application of esiRNAs to plants resulted in highly effective protection against massive CMV infection. However, optimal protection was achieved with newly designed multivalent "effective dsRNAs" (edsRNAs), which contain the sequences of several esiRNAs and are preferentially processed into precisely these esiRNAs. The esiRNA components can attack one or more target RNAs at different sites, be active in different silencing complexes and provide cross-protection against different viral variants, important properties for combating rapidly mutating pathogens such as CMV. esiRNAs and edsRNAs have thus been established as a new class of "RNA actives" that significantly increase the efficacy and specificity of RNA-mediated plant protection.

plant biology↗

bioRxiv2021

Expression levels of long noncoding natural antisense transcripts overlapping the UGT73C6 gene affect rosette size of Arabidopsis thaliana

Natural antisense long noncoding RNAs (lncNATs) are involved in the regulation of gene expression in plants, modulating different relevant developmental processes and responses to various stimuli. We identified and characterized two lncNATs (NAT1UGT73C6 and NAT2UGT73C6, collectively NATsUGT73C6) in Arabidopsis thaliana that are transcribed from a gene overlapping UGT73C6, a member of the UGT73C subfamily of genes encoding UDP-glycosyltransferases (UGTs). Expression of both NATsUGT73C6 is developmentally controlled and occurs independently of the transcription of UGT73C6 in cis. Downregulation of NATsUGT73C6 levels through artificial microRNAs results in a reduction of the rosette area, while constitutive overexpression of NAT1UGT73C6 or NAT2UGT73C6 leads to the opposite phenotype, an increase in rosette size. This activity of NATsUGT73C6 relies on its RNA sequence, and, although modulation of UGT73C6 in cis cannot be excluded, the observed phenotypes are not a consequence of the regulation of UGT73C6 in trans. The NATsUGT73C6 levels were shown to affect cell proliferation and thus individual leaf size. Consistent with this concept, our data suggest that the NATsUGT73C6 modulate the expression levels of key transcription factors involved in regulating leaf growth by modulating cell proliferation. These findings thus reveal an additional regulatory layer on the process of leaf growth.

plant biology↗