Biology subjects

Altegoer, F.

Publications and source records attributed to Altegoer, F..

10 recordsLinked to original sources

bioRxiv2026

A chromosome-scale super-pangenome of the lichen genus Peltigera reveals genome architecture and expanded interaction repertoires shared across pathogenic and mutualistic fungi

Fungi engage in associations with other organisms across a continuum from pathogenic to mutualistic lifestyles. Hence, they require a compendium of molecular capacities, including partner recognition, extracellular signaling, nutrient exchange, immune modulation, and control of microbial competitors. In filamentous pathogens such traits are frequently associated with compartmentalized genomes, including rapidly evolving secreted proteins known as effectors and expanded receptor families, but it remains unclear whether similar genomic principles shape mutualistic fungal symbioses. Here, we generated a chromosome-scale super-pangenome for the lichen-forming genus Peltigera, comprising 41 mycobiont assemblies representing eleven species, together with genomes of associated Nostoc and, in tripartite species, Coccomyxa photobionts. The mycobiont genomes revealed extensive variation in genome size, transposable element content, biosynthetic gene clusters, and lineage-specific gene content, with pronounced expansions in tripartite species. Across Peltigera, secreted protein encoding genes were preferentially located in TE-rich regions. We further identified Starship-like transposon elements, expanded antimicrobial protein repertoires, and a large, previously underestimated repertoire of fungal GPCRs dominated by Pth11-like receptors. Layer-specific transcriptomics of a P. rufescens thallus showed differential expression of several interaction-associated gene families, e.g. lectins, antimicrobial proteins and Pth11-like GPCRs. These data indicate that pathogenic and mutualistic fungi might exhibit shared genomic principles, including genome compartmentalization, mobile-element-associated diversification, and the expansion of molecular repertoires involved in recognition, extracellular control and signaling.

genomics↗

bioRxiv2026

Disentangling the sucrose metabolism of the corn smut Ustilago maydis reveals unexpected complexity

The race for carbohydrates shapes organismic interactions. In plant pathogenic fungi, sucrose is a key nutrient as it constitutes the major transport sugar in plants. Here, we investigate sucrose acquisition in the corn smut fungus Ustilago maydis, a biotrophic pathogen that transitions from yeast-like to hyphal growth for infection. We establish that the fungus encodes a secreted acidic invertase, Suc2, with a dimeric canonical glycoside hydrolase 32 architecture. Comparative biochemical analyses across fungal homologs indicate that this dimeric architecture represents the predominant state, whereas higher-order oligomers, as initially described for Saccharomyces cerevisiae Suc2, are restricted to a subset of lineages. Unexpectedly, elimination of Suc2 did not impair yeast-like growth on sucrose. Similarly, deletion of genes for sucrose transporter Srt1 and cytosolic hydrolase Suc1, typically associated with intracellular sucrose metabolism, did not abolish growth. Instead, sucrose utilization during yeast-like growth depended on a repurposed non-canonical module comprising maltose transporter Agt1 and intracellular (iso)maltases. In contrast, pathogenic development strongly relied on the canonical intracellular sucrose utilization pathway mediated by Srt1 and Agt1. Infection was strongly diminished in strains unable to metabolise sucrose, confirming its central nutritional role for the fungus. Together, our work defines the complete sucrose utilization repertoire of U. maydis and uncovers a lifestyle-dependent metabolic switch between alternative sucrose acquisition strategies. Flexible carbon acquisition might represent a widespread adaptive strategy in basidiomycete pathogenic fungi.

microbiology↗

bioRxiv2025

A co-evolved peptide-GPCR system senses host entry to drive fungal infection

A successful infection requires pathogens to recognize the specific host environment in order to reprogram their physiology accordingly. One major way in which eukaryotic cells sense their surroundings is via G-Protein Coupled Receptors (GPCRs), which share a seven-transmembrane architecture and G-protein-mediated downstream signaling. While mammalian GPCRs are well-characterized and represent important drug targets, their fungal counterparts remain poorly understood. In the corn pathogen Ustilago maydis, we now uncover a GPCR-based mechanism that allows the fungus to scout the host environment to sense whether it has entered into the plant tissue. During infection, the fungus secretes the protein Pit2, which is cleaved by host apoplastic-cysteine proteases, releasing a peptide ligand hidden within Pit2. This ligand activates the fungal GPCR Gpe1 strongly promoting fungal proliferation after initial host penetration. Comparative analyses reveal conservation of the Gpe1/Pit2 system, with co-evolutionary signatures preserving receptor-ligand specificity. Furthermore, this GPCR system recognizing hidden peptide ligands shows conceptual similarities to the fungal pheromone mating system, without sharing sequence similarity. Our findings reveal a co-evolved mechanism between fungus and host that encodes environmental context into a protein scaffold, establishing a novel paradigm for host-dependent signaling with implications for inter-organismic communication.

microbiology↗

bioRxiv2024

Jasmonic acid signalling is targeted by a smut fungal Tin2-fold effector

In plants, jasmonate signaling is a hub integrating environmental cues with growth and development. Due to its role in balancing defense responses against pathogens, it is a target of effector proteins from various pathogens. Here, we characterized the fungal effector protein Tue1 from the Brassicaceae smut fungus Thecaphora thlaspeos. T. thlaspeos naturally infects Arabis hirsuta but can also colonize the non-host Arabidopsis thaliana. In planta, the fungal protein Tue1 hijacks the plant importin- dependent nuclear transporter to reach the plant nucleus. It interacts with jasmonate ZIM domain 10 (JAZ10) proteins of both A. thaliana and Ar. hirsuta. Structure-guided analysis of Tue1 suggests that it binds the Jas motif of JAZ10 indicating a role in stabilization or binding competition with proteins like MYC3 and COI1. A subset of jasmonate-responsive genes is differentially regulated during T. thlaspeos infection, proposing a link of the Tue1 function to infection. Tue1 share structural similarity to the Tin2-fold family recently described in the corn smut Ustilago maydis. Our study therefore suggests that this structural effector family is expanded across fungal pathogens, although future studies have to reveal whether targeting JAZ-repressors is a conserved mechanism or specifically acquired as an adaptation to its perennial host.

biochemistry↗

bioRxiv2024

Deciphering the RNA-binding protein network during endosomal mRNA transport

Microtubule-dependent endosomal transport is crucial for polar growth, ensuring the precise distribution of cellular cargos such as proteins and mRNAs. However, the molecular mechanism linking mRNAs to the endosomal surface remains poorly understood. Here, we present a structural analysis of the key RNA-binding protein Rrm4 from Ustilago maydis. Our findings reveal a new type of MademoiseLLE domain featuring a seven-helical bundle that provides a distinct binding interface. A comparative analysis with the canonical MLLE domain of the poly(A)-binding protein Pab1 disclosed unique characteristics of both domains. Deciphering the MLLE binding code enabled prediction and verification of previously unknown Rrm4 interactors containing short linear motifs. Importantly, we demonstrated that the human MLLE domains, such as those of PABPC1 and UBR5, employed a similar principle to distinguish among interaction partners. Thus, our study provides unprecedented mechanistic insights into how structural variations in the widely distributed MLLE domain facilitates mRNA attachment during endosomal transport. SignificancePolar growing cells, such as fungal hyphae and neurons, utilize endosomes to transport mRNAs along their microtubules. But how do these mRNAs precisely attach to endosomes? Our study addresses this question by investing the key mRNA transporter, Rrm4, in a fungal model microorganism. We uncovered new features of a protein-protein interaction domain that recognizes specific short linear motifs in binding partners. While this domain resembles one found in the poly(A)-binding protein, it exhibits distinct motif recognition. Deciphering the underlying binding code unveiled new interaction partners for Rrm4. The recognition system is used to form a resilient network of RNA-binding proteins (RBPs) and their interaction partners during endosomal transport. This principle is applicable to humans, highlighting its fundamental importance.

microbiology↗

bioRxiv2024

The fungal protein Jps1 facilitates unconventional protein secretion through a direct phosphoinositide interaction

Protein secretion is indispensable for essential cellular processes in eukaryotic cells, contributing significantly to nutrient acquisition, defense or communication. Alternative pathways bypassing the endomembrane system collectively referred to as unconventional secretion are gaining increasing attention. A number of important molecules such as cytokines, fibroblast growth factor or viral proteins are being exported through these mechanistically diverse pathways. In the fungal model Ustilago maydis, cytokinesis-dependent unconventional secretion mediates export of the chitinase Cts1 via the fragmentation zone. This membrane-rich compartment is formed during cytokinesis between mother and daughter cells. Recently, we identified Jps1, a previously uncharacterized protein, as a crucial factor for Cts1 localization and export. Combining biochemical experiments and in vivo studies, we here uncover two pivotal features of Jps1: dimerization and phosphoinositide (PIP) binding. Our findings reveal that a conserved structural core domain mediates homodimerization, while surrounding flexible variable regions suggest potential diversification in different basidiomycete species. Jps1 does not harbor a canonical PIP-binding domain but instead specificity of the interaction with the preferred PIP PI(4,5)P2 is determined by basic residues. Importantly, loss of PI(4,5)P2 binding specificity results in mis-localisation, morphological defects and reduced extracellular Cts1 activity, particularly at low cell densities. This discovery sheds light on previously unknown key features of Jps1, elucidating its role in supporting Cts1 secretion, and representing a crucial step towards understanding the broader implications of unconventional secretion in eukaryotic cells.

biochemistry↗

bioRxiv2022

Structural and functional analysis of the cerato-platanin-like effector protein Cpl1 suggests diverging functions in smut fungi

Plant pathogenic fungi are causative agents of the majority of plant diseases and can lead to severe crop loss in infected populations. Fungal colonization is achieved by combining different strategies, such as avoiding and counteracting the plant immune system and manipulating the host metabolome. Of major importance are effector proteins secreted by the fungi that fulfill diverse functions to support the infection process. Most of these proteins are highly specialized and structural and biochemical information is often absent. Here, we present the atomic structures of the cerato-platanin-like protein Cpl1 from Ustilago maydis and its homolog Uvi2 from Ustilago hordei. Both proteins adopt a double-{Psi}-{beta}-barrel architecture reminiscent of cerato-platanin proteins, a class so far not described in smut fungi. Our structure-function analysis shows that Cpl1 binds to soluble chitin fragments via two extended grooves at the dimer interface of the two monomer molecules. This carbohydrate-binding mode has not been observed previously and expands the repertoire of chitin-binding proteins. Cpl1 localizes to the cell wall of U. maydis and specifically enriches cell-wall degrading and -decorating proteins during maize infection. The architecture of Cpl1 harboring four surface exposed loop regions supports the idea that it might play a role in spatial coordination of these proteins. While deletion of cpl1 has only mild effects on the virulence of U. maydis, a recent study showed that deletion of uvi2 strongly impairs U. hordei virulence. Our structural comparison between Cpl1 and Uvi2 reveals sequence variations in the loop regions which might explain a diverging function.

biochemistry↗

bioRxiv2021

Structure and mechanistic features of the prokaryotic minimal RNase P

Endonucleolytic removal of 5-leader sequences from tRNA precursor transcripts (pre-tRNAs) by RNase P is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein-only versions of the enzyme exert this function in various Eukarya (there termed PRORPs) and in some bacteria (Aquifex aeolicus and close relatives); both enzyme types belong to distinct subgroups of the PIN domain metallonuclease superfamily. Homologs of Aquifex RNase P (HARPs) are also expressed in some other bacteria and many archaea, where they coexist with RNA-based RNase P and do not represent the main RNase P activity. Here we solved the structure of the bacterial HARP from Halorhodospira halophila by cryo-EM revealing a novel screw-like dodecameric assembly. Biochemical experiments demonstrate that oligomerization is required for RNase P activity of HARPs. We propose that the tRNA substrate binds to an extended spike-helix (SH) domain that protrudes from the screw-like assembly to position the 5-end in close proximity to the active site of the neighboring dimer subunit. The structure suggests that eukaryotic PRORPs and prokaryotic HARPs recognize the same structural elements of pre-tRNAs (tRNA elbow region and cleavage site). Our analysis thus delivers the structural and mechanistic basis for pre-tRNA processing by the prokaryotic HARP system.

biochemistry↗

bioRxiv2021

The CTPase activity of ParB acts as a timing mechanism to control the dynamics and function of prokaryotic DNA partition complexes

DNA partitioning CTPases of the ParB family mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromeric region of target DNA molecules and then spread laterally to form large nucleoprotein complexes that serve as docking points for the DNA segregation machinery. Here, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. Moreover, we solve crystal structures of ParB in the pre- and post-hydrolysis state and provide insights into the catalytic mechanism underlying nucleotide hydrolysis. The characterization of CTPase-deficient ParB variants reveals that CTP hydrolysis serves as a timing mechanism to control the sliding time of ParB. Hyperstable clamps are trapped on the DNA, leading to excessing spreading and severe chromosome segregation defects in vivo. These findings clarify the role of the ParB CTPase cycle in partition complex dynamics and function and thus complete our understanding of this prototypic CTP-dependent molecular switch.

microbiology↗

bioRxiv2021

Identification and characterization of two transmembrane proteins required for virulence of Ustilago maydis

Smut fungi comprise a large group of biotrophic phytopathogens infecting important crops such as wheat and corn. Through the secretion of effector proteins, the fungus actively suppresses plant immune reactions and modulates its hosts metabolism. Consequently, how soluble effector proteins contribute to virulence is already characterized in a range of phytopathogens. However, membrane-associated virulence factors have been much less studied to date. Here, we investigated six transmembrane (TM) proteins that show elevated gene expression during biotrophic development of the maize pathogen Ustilago maydis. We show that two of the six proteins, named Vmp1 and Vmp2 (virulence-associated membrane protein), are essential for the full virulence of U. maydis. The deletion of the corresponding genes lead to a substantial attenuation in the virulence of U. maydis. Furthermore, both are conserved in various related smuts and contain no domains of known function. Our biochemical analysis clearly shows that Vmp1 and Vmp2 are membrane-associated proteins, potentially localizing to the U. maydis plasma membrane. Mass photometry and light scattering suggest that Vmp1 mainly occurs as a monomer, while Vmp2 is dimeric. Notably, the large and partially unstructured C-terminal domain of Vmp2 is crucial for virulence while not contributing to dimerization. Taken together, we here provide an initial characterization of two membrane proteins as virulence factors of U. maydis.

plant biology↗