Biology subjects

Isaksson, J.

Publications and source records attributed to Isaksson, J..

8 recordsLinked to original sources

bioRxiv2025

Dual recognition of structurally unrelated mildew effectors underlies the broad-spectrum resistance of Pm3e in wheat

Broad-spectrum resistance genes are highly valuable for sustainable crop protection, yet the molecular basis of their activity is often unknown. The Pm3 allelic series in wheat encodes NLR receptors that recognize avirulence (AVR) effectors of wheat powdery mildew. Here, we show that near-identical Pm3 alleles vary greatly in resistance efficacy and broadness against a global mildew isolate collection and subsequently use this model system to study the mechanisms underlying broad-spectrum resistance. We demonstrate that two alleles, Pm3d and Pm3e, provide resistance against the majority of isolates worldwide, by each recognizing two AVR effectors from powdery mildew, thereby lowering the risk of resistance breakdown. While Pm3d recognizes two closely related RNase-like AVR effectors, Pm3e detects two structurally diverse AVRs, including an effector belonging to a large, uncharacterized protein family with a novel structural fold. Using chimeric Pm3 NLRs, we identify specificity-defining polymorphisms of Pm3d and Pm3e against their diverse effector targets. Lastly, we demonstrate that Pm3d and Pm3e activities can be combined in engineered Pm3 NLRs, thereby further extending their recognition spectrum. Our findings highlight the potential of Pm3 immune receptors for long-lasting wheat protection by demonstrating their versatility in recognizing structurally diverse effectors and their amenability to NLR engineering.

plant biology↗

bioRxiv2025

Virulence on Pm4 kinase-based resistance is determined by two divergent wheat powdery mildew effectors

The wheat resistance gene Pm4 encodes a kinase fusion protein and has gained particular attention as it confers race-specific resistance against two major wheat pathogens: powdery mildew and blast. Here, we describe the identification of AvrPm4, the mildew avirulence effector recognised by Pm4, using UV- mutagenesis, and its functional validation in wheat protoplasts. We show that AvrPm4 directly interacts with and is phosphorylated by Pm4. Using genetic association and QTL mapping, we furthermore demonstrate that evasion of Pm4 resistance by virulent mildew isolates relies on a second fungal component, SvrPm4, which suppresses AvrPm4-induced cell death. Surprisingly, SvrPm4 was previously described as AvrPm1a. We show that SvrPm4, but not its inactive variant svrPm4, is recognised by the NLR immune receptor Pm1a. These multiple roles of a single effector provide a new perspective on fungal (a)virulence proteins and their combinatorial interactions with different types of immune receptors.

genetics↗

bioRxiv2024

Interactions of sequence diverse effector proteins of wheat powdery mildew control recognition specificity by the corresponding immune receptor

To successfully colonize the living tissue of its host, the fungal wheat powdery mildew pathogen produces diverse effector proteins that are suggested to reprogram host defense responses and physiology. When recognized by host immune receptors, these proteins become avirulence (AVR) effectors. Several sequence-diverse AVRPM3 effectors and the suppressor of AVRPM3-PM3 recognition (SVRPM3a1/f1) are involved in triggering allele-specific, Pm3-mediated resistance, but the molecular mechanisms controlling their function in the host cell remain unknown. Here, we describe that AVRPM3b2/c2, AVRPM3a2/f2 and SVRPM3a1/f1 form homo- and heteromeric complexes with each other, suggesting they are present as dimers in the host cell. Alphafold2 modelling substantiated previous predictions that AVRPM3b2/c2, AVRPM3a2/f2 and SVRPM3a1/f1 all adopt a core RNase-like fold. We found that a single amino acid mutation in a predicted surface exposed region of AVRPM3a2/f2 resulted in recognition by the PM3b immune receptor, which does not recognize wildtype AVRPM3a2/f2. This indicates that differential AVRPM3 recognition by variants of the highly related PM3 immune receptors is due to subtle differences in similar protein surfaces of sequence-diverse AVRs. Based on our findings, we propose a model in which homodimers of AVRPM3s are recognized by their corresponding PM3 variants and that heterodimer formation with SVRPM3a1/f1 allows for evasion of recognition.

plant biology↗

bioRxiv2024

A reference metagenome sequence of the lichen Cladonia rangiformis

[bullet] Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis. [bullet]Using long read sequences from an entire symbiotic complex, plus short read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. [bullet]We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises [~]22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. [bullet]Our study revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria.

evolutionary biology↗

bioRxiv2024

The wheat NLR protein PM3b localizes to endoplasmic reticulum-plasma membrane contact sites and interacts with AVRPM3b2/c2 through its LRR domain.

Plant nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular immune receptors that directly or indirectly perceive pathogen derived effector proteins to induce an immune response. NLRs display diverse sub-cellular localizations, which are associated with the capacity of the immune receptor to confer disease resistance and recognize its corresponding avirulence effector. In wheat, the NLR PM3b recognizes the wheat powdery mildew effector AVRPM3b2/c2 and we examined the molecular mechanism underlying this recognition. We show that PM3b and other PM3 variants localize to endoplasmic reticulum (ER)-plasma membrane (PM) contact sites (EPCS) while AVRPM3b2/c2 localizes to the nucleocytoplasmic space. Additionally, we found that PM3b interacts in planta with AVRPM3b2/c2 through its LRR domain. We further demonstrate that full length PM3b interaction with AVRPM3b2/c2 is considerably weaker than for the isolated PM3b LRR domain or the susceptible PM3 variant PM3CS, indicating that activation of PM3b leads to dissociation of the complex. In line with this: We observed a strong interaction between PM3b and AVRPM3b2/c2 in a P-loop mutant of PM3b which was unable to initiate a cell death response, or when an inactive variant of AVRPM3b2/c2 was used. We propose that PM3b transiently interacts with AVRPM3b2/c2 through residues in the LRR which are conserved among PM3 variants while the amino acids necessary for full activation and cell death signaling are unique to PM3b. Our data suggests that PM3b localization and interaction with AVRPM3b2/c2 differs from other well studied NLRs and further highlights the mechanistic diversity in NLR-mediated responses against pathogens in plants.

plant biology↗

bioRxiv2023

Outer membrane vesicles as realistic models of bacterial membranes in interaction studies by Surface Plasmon Resonance

One way to mitigate the ongoing antimicrobial resistance crisis is to discover and develop new classes of antibiotics. As all antibiotics at some point needs to either cross or interact with the bacterial membrane, there is a need for representative models of bacterial membranes and efficient methods to characterize the interactions to novel antimicrobials - both to generate new knowledge and to screen compound libraries. Since the bacterial cell envelope is a complex assembly of lipids, lipopolysaccharides, membrane proteins and other components, constructing realistic synthetic liposome-based models of the membrane is both difficult and expensive. We here propose to let the bacteria do the hard work for us. Outer membrane vesicles (OMVs) are naturally secreted by Gram-negative bacteria, playing a role in communication between bacteria, as virulence factors, molecular transport or being a part of the antimicrobial resistance mechanism. OMVs consist of the bacterial outer membrane and thus inherit many components and properties of the native outer cell envelope. In this work we have isolated and characterized OMVs from E. coli mutant strains and clinical isolates of the ESKAPE members Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa. The OMVs were shown to be representative models for the bacterial membrane in terms of lipid composition with strain specific variations. The OMVs were further used to probe the interactions between OMV and antimicrobial peptides (AMPs) as model compounds by Surface Plasmon Resonance (SPR) and provide proof-of-principle that OMVs can be used as an easily accessible and highly realistic model for the bacterial surface in interaction studies. This further enables direct monitoring of the effect of induction by antibiotics, or the response to host-pathogen interactions.

molecular biology↗

bioRxiv2022

Deficiency of Heterogeneous Nuclear Ribonucleoprotein U leads to delayed neurogenesis

Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level. HNRNPU downregulation leads to altered neurogenesis and an increased fraction of neural progenitors in the maturing neuronal population. We conclude that, HNRNPU locus is involved in delayed commitment of neural progenitors to neuronal maturation in cell types with hindbrain profile.

neuroscience↗

bioRxiv2021

Standing genetic variation of the AvrPm17 avirulence gene in powdery mildew limits the effectiveness of an introgressed rye resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable - a phenomenon that remains poorly understood as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used QTL mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of re-occurring gene conversion events and are members of a mildew sub-lineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sub-lineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangle complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations becomes an integral part of introgression breeding to ensure effective and durable resistance in wheat. Significance StatementDomesticated and wild wheat relatives provide an important source of new immune receptors for wheat resistance breeding against fungal pathogens. The durability of these resistance genes is variable and difficult to predict, yet it is crucial for effective resistance breeding. We identified a fungal effector protein recognised by an immune receptor introgressed from rye to wheat. We found that variants of the effector allowing the fungus to overcome the resistance are ancient. They were already present in the wheat powdery mildew gene pool before the introgression of the immune receptor and are therefore responsible for the rapid resistance breakdown. Our study demonstrates that the effort to identify new resistance genes should be accompanied by studies of avirulence genes on the pathogen side.

plant biology↗