Structure of Ustilago maydis killer toxin KP6 alpha-subunit. A multimeric assembly with a central pore

Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors

Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors are engaged in a molecular arms race with the host resulting in conflicting evolutionary constraints to manipulate host cells without triggering immune responses. The molecular mechanisms allowing effectors to be at the same time robust and evolvable remain largely enigmatic. Here, we show that 62 conserved structure-related families encompass the majority of fungal orphan effector candidates in the Pezizomycotina subphylum. These effectors diversified through changes in patterns of thermodynamic frustration at surface residues. The underlying mutations tended to increase the robustness of the overall effector protein structure while switching potential binding interfaces. This mechanism could explain how conserved effector families maintained biological activity over long evolutionary timespans in different host environments and provides a model for the emergence of sequence-unrelated effector families with conserved structures.

The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

BACKGROUND

Scab, caused by the biotrophic fungus Venturia inaequalis, is the most economically important disease of apples worldwide. During infection, V. inaequalis occupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth by V. inaequalis, as well as in activating, suppressing, or circumventing resistance protein-mediated defences in apple, is required.

RESULTS

We generated the first comprehensive RNA-seq transcriptome of V. inaequalis during colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid, or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector from Leptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi.

CONCLUSIONS

Our study reveals the transcriptomic profile underpinning subcuticular growth by V. inaequalis and provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins.

Genomic discovery and structural dissection of a novel type of polymorphic toxin system in gram-positive bacteria

Bacteria have developed several molecular conflict systems to facilitate kin recognition and non-kin competition to gain advantages in the acquisition of growth niches and of limited resources. One such example is a large class of so-called polymorphic toxin systems (PTSs), which comprise a variety of the toxin proteins secreted via T2SS, T5SS, T6SS, T7SS and many others. These systems are highly divergent in terms of sequence/structure, domain architecture, toxin-immunity association, and organization of the toxin loci, which makes it difficult to identify and characterize novel systems using traditional experimental and bioinformatic strategies. In recent years, we have been developing and utilizing unique genome-mining strategies and pipelines, based on the organizational principles of both domain architectures and genomic loci of PTSs, for an effective and comprehensive discovery of novel PTSs, dissection of their components, and prediction of their structures and functions. In this study, we present our systematic discovery of a new type of PTS (S8-PTS) in several gram-positive bacteria. We show that the S8-PTS contains three components: a peptidase of the S8 family (subtilases), a polymorphic toxin, and an immunity protein. We delineated the typical organization of these polymorphic toxins, in which a N-terminal signal peptide is followed by a potential receptor binding domain, BetaH, and one of 16 toxin domains. We classified each toxin domain by the distinct superfamily to which it belongs, identifying nine BECR ribonucleases, one Restriction Endonuclease, one HNH nuclease, two novel toxin domains homologous to the VOC enzymes, one toxin domain with the Frataxin-like fold, and several other unique toxin families such as Ntox33 and HicA. Accordingly, we identified 20 immunity families and classified them into different classes of folds. Further, we show that the S8-PTS-associated peptidases are analogous to many other processing peptidases found in T5SS, T7SS, T9SS, and many proprotein-processing peptidases, indicating that they function to release the toxin domains during secretion. The S8-PTSs are mostly found in animal and plant-associated bacteria, including many pathogens. We propose S8-PTSs will facilitate the competition of these bacteria with other microbes or contribute to the pathogen-host interactions.

Specific Hypersensitive Response-Associated Recognition of New Apoplastic Effectors from Cladosporium fulvum in Wild Tomato

Tomato leaf mold disease is caused by the biotrophic fungus Cladosporium fulvum. During infection, C. fulvum produces extracellular small secreted protein (SSP) effectors that function to promote colonization of the leaf apoplast. Resistance to the disease is governed by Cf immune receptor genes that encode receptor-like proteins (RLPs). These RLPs recognize specific SSP effectors to initiate a hypersensitive response (HR) that renders the pathogen avirulent. C. fulvum strains capable of overcoming one or more of all cloned Cf genes have now emerged. To combat these strains, new Cf genes are required. An effectoromics approach was employed to identify wild tomato accessions carrying new Cf genes. Proteomics and transcriptome sequencing were first used to identify 70 apoplastic in planta-induced C. fulvum SSPs. Based on sequence homology, 61 of these SSPs were novel or lacked known functional domains. Seven, however, had predicted structural homology to antimicrobial proteins, suggesting a possible role in mediating antagonistic microbe-microbe interactions in planta. Wild tomato accessions were then screened for HR-associated recognition of 41 SSPs, using the Potato virus X-based transient expression system. Nine SSPs were recognized by one or more accessions, suggesting that these plants carry new Cf genes available for incorporation into cultivated tomato.

The mechanism of toxicity in HET-S/HET-s prion incompatibility

The HET-s protein from the filamentous fungus Podospora anserina is a prion involved in a cell death reaction termed heterokaryon incompatibility. This reaction is observed at the point of contact between two genetically distinct strains when one harbors a HET-s prion (in the form of amyloid aggregates) and the other expresses a soluble HET-S protein (96% identical to HET-s). How the HET-s prion interaction with HET-S brings about cell death remains unknown; however, it was recently shown that this interaction leads to a relocalization of HET-S from the cytoplasm to the cell periphery and that this change is associated with cell death. Here, we present detailed insights into this mechanism in which a non-toxic HET-s prion converts a soluble HET-S protein into an integral membrane protein that destabilizes membranes. We observed liposomal membrane defects of approximately 10 up to 60 nm in size in transmission electron microscopy images of freeze-fractured proteoliposomes that were formed in mixtures of HET-S and HET-s amyloids. In liposome leakage assays, HET-S has an innate ability to associate with and disrupt lipid membranes and that this activity is greatly enhanced when HET-S is exposed to HET-s amyloids. Solid-state nuclear magnetic resonance (NMR) analyses revealed that HET-s induces the prion-forming domain of HET-S to adopt the β-solenoid fold (previously observed in HET-s) and this change disrupts the globular HeLo domain. These data indicate that upon interaction with a HET-s prion, the HET-S HeLo domain partially unfolds, thereby exposing a previously buried ∼34-residue N-terminal transmembrane segment. The liberation of this segment targets HET-S to the membrane where it further oligomerizes, leading to a loss of membrane integrity. HET-S thus appears to display features that are reminiscent of pore-forming toxins.

The atomic structure of the virally encoded antifungal protein, KP6

Killer toxins are produced by several genera of yeast and filamentous fungi. A small proportion of Ustilago maydis strains produce killer toxins, to which they are resistant, but sensitive strains are the majority in the wild populations. There are three killer types (P1, P4 and P6) that secrete KP1, KP4 and KP6 toxins, respectively, which are produced only by strains persistently infected with double-stranded RNA viruses (UmV) in the cell cytoplasm. Unlike nearly all other viruses, UmV are only transmitted through mitosis or meiosis. As shown here, KP6 is different from any other known cytotoxic protein. KP6 is neutral protein composed of two subunits: KP6α and KP6β. KP6α is responsible for targeting while KP6β is cytotoxic. Neither subunit is homologous in either sequence or structure to any other toxin, but they have highly similar structures to each other. The major difference between the two subunits is a hydrophobic helix at the N-terminus of KP6α and is likely key to target recognition. Unlike any other toxin, KP6 is translated as a single polypeptide with a 31-residue linker region in the middle of the protein. From structural prediction studies, this linker likely makes for a more compact KP6 structure that sequesters the hydrophobic helix of KP6α. A model whereby the protoxin undergoes a conformational activation process that exposes this helix immediately prior to secretion is presented.

Mycoviruses: future therapeutic agents of invasive fungal infections in humans?

Invasive fungal infections are relatively common opportunistic infections in immunocompromised patients and are still associated with a high mortality rate. Furthermore, these infections are often complicated by resistance or refractoriness to current antimicrobial agents. Therefore, an urgent need exists for new therapeutic strategies based on the identification of new microbial targets and novel antimicrobial agents. One such hypothetical therapeutic strategy may involve the use of mycoviruses that are able to selectively infect fungi. Current knowledge of mycoviruses of human pathogenic fungi and the scope for using (recombinant) mycoviruses as future biological control agents are reviewed here.

An improved phage-display panning method to produce an HM-1 killer toxin anti-idiotypic antibody

BACKGROUND

Phage-display panning is an integral part of biomedical research. Regular panning methods are sometimes complicated by inefficient detachment of the captured phages from the antigen-coated solid supports, which prompted us to modify. Here, we produce an efficient antigen-specific single chain fragment variable (scFv) antibody by using a target-related molecule that favored selection of recombinant antibodies.

RESULTS

To produce more selective and specific anti-idiotypic scFv-antibodies from a cDNA library, constructed from HM-1 killer toxin (HM-1)-neutralizing monoclonal antibodies (nmAb-KT), the method was modified by using an elution buffer supplemented with HM-1 that shares structural and functional similarities with the active site of the scFv antibody. Competitive binding of HM-1 to nmAb-KT allowed easy and quick dissociation of scFv-displayed phages from immobilized nmAb-KT to select specific anti-idiotypic scFv antibodies of HM-1. After modified panning, 80% clones (40/50) showed several times higher binding affinity to nmAb-KT than regular panning. The major populations (48%) of these clones (scFv K1) were genotypically same and had strong cytocidal activity against Saccharomyces and Candida species. The scFv K1 (K(d) value = 4.62 x 10(-8) M) had strong reactivity toward nmAb-KT, like HM-1 (K(d) value = 6.74 x 10(-9) M) as judged by SPR analysis.

CONCLUSION

The scFv antibodies generated after modified subtractive panning appear to have superior binding properties and cytocidal activity than regular panning. A simple modification of the elution condition in the phage-display panning protocol makes a large difference in determining success. Our method offers an attractive platform to discover potential therapeutic candidates.

Castles and cuitlacoche: the first international Ustilago conference

The first international Ustilago conference was held in Marburg, Germany from August 22 to 25, 2002. The meeting focused on molecular genetic and cell biology research with Ustilago maydis, the causative agent of common smut of maize. This fungus has emerged as a useful experimental organism for studying the biology of basidiomycete fungi, with a particular emphasis on the interaction of the fungus with the host plant. Thus presentations at the meeting covered the range of current research topics including DNA recombination and repair, mating and sexual development, phytopathology, cell biology, the cell cycle, signaling, and genomics. The meeting also highlighted historical aspects of U. maydis research with presentations by pioneers in the field including Robin Holiday (recombination), Yigal Koltin (killer phenomenon) and Peter Day (plant pathology).

The Ustilaginales as plant pests and model systems

The Ustilaginales are a vast and diverse group of fungi, which includes the plant pathogenic smuts that cause significant losses to crops worldwide. Members of the Ustilaginales are also valuable models for the unraveling of fundamental mechanisms controlling important biological processes. Ustilago maydis is an important fungal model system and has been well studied with regard to mating, morphogenesis, pathogenicity, signal transduction, mycoviruses, DNA recombination, and, recently, genomics. In this review we discuss the life cycles of members of the Ustilaginales and provide background on their economic impact as agricultural pests. We then focus on providing a summary of the literature with special attention to topics not well covered in recent reviews such as the use of U. maydis in mycovirus research and as a model for understanding the molecular mechanisms of fungicide resistance and DNA recombination and repair.

Liposomes as formulation excipients for protein pharmaceuticals: a model protein study

PURPOSE

The advent of recombinant DNA technology has made possible the pharmaceutical use of a wide range of proteins and peptides. However, the complex structure of proteins renders them susceptible to physical instabilities such as denaturation, aggregation and precipitation. We tested the hypothesis that partial unfolding and exposure of hydrophobic domains leads to physical instability, and investigated approaches to stabilize protein formulations.

METHODS

KP6 beta, an 81 amino acid killer toxin from Ustilago maydis, was used as a model protean. Circular dichroism and fluorescence spectroscopy were used to study the temperature dependent folding/ unfolding characteristics of KP6 beta. ANS (1,8 anilinonaphthalene sulfonate), a fluorescent probe that partitions into hydrophobic domains, was used to detect exposure of hydrophobic domains.

RESULTS

As the temperature was elevated, near-UV CD indicated progressive loss of KP6 beta tertiary structure, while far-UV CD indicated retention of secondary structure. Increasing exposure of hydrophobic domains was observed, as indicated by the penetration of ANS. At elevated temperatures (60 degrees C), KP6 beta3 conserved most secondary structural features. However, tertiary structure was disordered, suggesting the existence of a partially folded, structured intermediate state. Liposomes bound to partially unfolded structures and prevented the formation of aggregates.

CONCLUSIONS

Partial unfolding resulted in increased exposure of hydrophobic domains and aggregation of KP6 beta, but with preservation of secondary structure. Liposomes interacted with the structured intermediate state, stabilizing the protein against aggregation. These results suggest a general formulation strategy for proteins, in which partially unfolded structures are stabilized by formulation excipients that act as molecular chaperones to avoid physical instability.