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At least 19 recordsLinked to original sources
PubMed2025

Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages.

BACKGROUND: Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). In Magnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking. RESULTS: Here, we focus on 16 AVR effector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies from publicly available short-read sequencing data across all major M. oryzae lineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among lineages. Next, we determined AVR gain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. Each AVR was integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversify AVR loci. We used the large genomic dataset to recapitulate the evolution of the rice blast AVR1-CO39 locus. CONCLUSIONS: Taken together, our work demonstrates how TE dynamics are an integral component of M. oryzae effector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.

Ascomycota↗
PubMed1985

Evolution of antibody structure and effector functions: comparative hemolytic activities of monomeric and tetrameric IgM from rainbow trout, Salmo gairdnerii.

Monomeric and tetrameric IgM anti-haptin antibodies isolated from the sera of rainbow trout (S. gairdnerii) by immunoaffinity chromatography were compared both immunochemically and with regard to their functional abilities to lyse haptenated trout erythrocytes in the presence of trout complement. The two populations had similar binding affinities for hapten and apparently identical L chains, but differed in H chain peptide maps and immunoreactivity with rabbit anti-trout H chain serum. These differences could not be attributed to J-chain. The abilities of the two antibody subpopulations to activate C to lyse haptenated trout erythrocytes also differed dramatically. Such functional differences are not simply explained by the greater avidity of the tetrameric form since preliminary studies show that the monomeric form of trout IgM activates C via an alternative pathway mechanism while the tetrameric form activates both classical and alternative pathway mechanisms. Results suggest divergent evolution of antibody structures involved in the familiar effector functions (C activation, transport, etc.).

Animals↗
PubMed2026

Evolutionary constraints and regulatory plasticity shape host specialization in the Magnaporthe oryzae species complex.

Rice blast caused by Magnaporthe oryzae threatens global rice production, and wheat blast emergence highlights the pathogen's capacity for host shifts. Although numerous studies have described M. oryzae genome organization and infection mechanisms, critical questions remain regarding the evolutionary drivers of stable host specialization. Importantly, the blast pathogen comprises a species complex of genetically differentiated, host-adapted lineages rather than single homogeneous species. To address this knowledge gap, we integrate evidence from evolutionary genomics, transcriptomics, and metabolomics to develop the "Constrained Plasticity" framework. We argue that host adaptation arises from three interacting layers: genomic scaffolding (including epigenetic and noncoding RNA regulation), regulatory networks (enabling transcriptional plasticity), and metabolic compatibility (determining physiological success). This systems-level perspective explains the long-term stability of host-adapted lineages and the rare breakdowns resulting in host shifts, such as wheat blast. This framework generates testable predictions for pathogen emergence and provides a roadmap for developing lineage-aware resistance strategies.

Oryza↗
PubMed2024

A gene with a thousand alleles: The hyper-variable effectors of plant-parasitic nematodes.

Pathogens are engaged in a fierce evolutionary arms race with their host. The genes at the forefront of the engagement between kingdoms are often part of diverse and highly mutable gene families. Even in this context, we discovered unprecedented variation in the hyper-variable (HYP) effectors of plant-parasitic nematodes. HYP effectors are single-gene loci that potentially harbor thousands of alleles. Alleles vary in the organization, as well as the number, of motifs within a central hyper-variable domain (HVD). We dramatically expand the HYP repertoire of two plant-parasitic nematodes and define distinct species-specific "rules" underlying the apparently flawless genetic rearrangements. Finally, by analyzing the HYPs in 68 individual nematodes, we unexpectedly found that despite the huge number of alleles, most individuals are germline homozygous. These data support a mechanism of programmed genetic variation, termed HVD editing, where alterations are locus specific, strictly governed by rules, and theoretically produce thousands of variants without errors.

Animals↗
PubMed2026

Conserved protein folds underpin the diversification of secreted proteins in a fungal pathogen.

BACKGROUND: During host colonization, fungal plant pathogens secrete effector-like proteins that alter host cell physiology and target plant-associated microbes. However, rapid evolution and low sequence conservation hinder the study and characterization of these proteins. The fungus Zymoseptoria passerinii infects Hordeum spp. and includes lineages adapted to wild and domesticated barley. To date, the evolution of effector-like proteins in this species has not been addressed. RESULTS: We combined multiple structure-based and network analyses to unravel the secretome of Z. passerinii. We first compared AlphaFold2 and ESMFold predictions to establish the baseline for structural analyses. We identified 72 structural clusters in the secretome, revealing fold-level relationships across divergent sequences. We showed that effector-like proteins with predicted host immune-interfering functions evolved from a limited group of protein folds, whereas proteins with predicted antimicrobial properties were distributed across fold groups. Physicochemical comparisons indicate that putative antimicrobial effectors predominantly emerged through amino acid replacements on common effector-enriched scaffolds in Z. passerinii, reconfiguring surface charge and electrostatics. We analyzed intra- and interspecific variation in selected effector-enriched families by comparing Z. passerinii proteins and homologs across the genus Zymoseptoria. We describe constrained core folds, with local variation in loop and surface-exposed regions, consistent with fold stability while still enabling protein diversification. We further report that putative antimicrobial effector homologs are broadly distributed across the genus despite sequence divergence. CONCLUSIONS: The secretome of Z. passerinii is organized around common structural folds that support diverse biological roles, including host manipulation and host-associated microbial interactions. Conserved scaffolds combined with surface and physicochemical variation likely contribute to rapid adaptive evolution of effector-like proteins in Z. passerinii.

Fungal Proteins↗
PubMed1992

Evolution of secondary metabolite production: potential roles for antibiotics as prebiotic effectors of catalytic RNA reactions.

It has been proposed that organic molecules related to known secondary metabolites have existed since the beginning of biochemical evolution and were present in primordial soups. Under primitive earth conditions certain of these molecules may have played roles as effectors in prebiotic reactions, especially those involving catalytic RNA (ribozymes). We demonstrate that a number of antibiotic-related secondary metabolites bind to group I introns and either inhibit splicing reactions or promote the formation of intron oligomers. This is consistent with the functional co-evolution of catalytic RNA and secondary metabolites as antibiotic inhibitors of translation, and supports the notion of an evolutionary relationship between group I introns and ribosomal RNA.

Anti-Bacterial Agents↗
PubMed2025

Diversification, loss, and virulence gains of the major effector AvrStb6 during continental spread of the wheat pathogen Zymoseptoria tritici.

Interactions between plant pathogens and their hosts are highly dynamic and mainly driven by pathogen effectors and plant receptors. Host-pathogen co-evolution can cause rapid diversification or loss of pathogen genes encoding host-exposed proteins. The molecular mechanisms that underpin such sequence dynamics remains poorly investigated at the scale of entire pathogen species. Here, we focus on AvrStb6, a major effector of the global wheat pathogen Zymoseptoria tritici, evolving in response to the cognate receptor Stb6, a resistance widely deployed in wheat. We comprehensively captured effector gene evolution by analyzing a global thousand-genome panel using reference-free sequence analyses. We found that AvrStb6 has diversified into 59 protein isoforms with a strong association to the pathogen spreading to new continents. Across Europe, we found the strongest differentiation of the effector consistent with high rates of Stb6 deployment. The AvrStb6 locus showed also a remarkable diversification in transposable element content with specific expansion patterns across the globe. We detected AvrStb6 gene losses and evidence for transposable element-mediated disruptions. We used virulence datasets of genome-wide association mapping studies to predict virulence changes across the global panel. Genomic predictions suggested marked increases in virulence on Stb6 cultivars concomitant with the spread of the pathogen to Europe and the subsequent spread to further continents. Finally, we genotyped French bread wheat cultivars for Stb6 and monitored resistant cultivar deployment concomitant with AvrStb6 evolution. Taken together, our data provides a comprehensive view of how a rapidly diversifying effector locus can undergo large-scale sequence changes concomitant with gains in virulence on resistant cultivars. The analyses highlight also the need for large-scale pathogen sequencing panels to assess the durability of resistance genes and improve the sustainability of deployment strategies.

Ascomycota↗
PubMed1988

Induction of cell-mediated cytotoxicity by shark 19S IgM.

Plasma from unimmunized nurse sharks can mediate a reaction similar to antibody-dependent cell-mediated cytotoxicity (ADCC). Normal shark plasma contains numerous natural antibodies reactive with a variety of antigens, including the target employed. Adsorption of plasma with target cells removed a significant amount of activity, suggesting involvement of antibody. Purified 19s IgM was shown to be a component of shark plasma capable of inducing cytotoxicity. These cytotoxic reactions differ from observations in homeothermic vertebrates in that shark immunoglobulin appears to bind more avidly to the effector cells than to the targets. The effector leukocytes are glass adherent, but not susceptible to carbonyl iron treatment, which clearly separates them from the phagocytic effectors of spontaneous cytotoxicity. Thus, the shark possesses leukocytes with the capability of mediating an ADCC-like reaction. These leukocytes, in concert with those mediating spontaneous cytotoxicity, could provide the shark with an effective immunosurveillance system. These data also indicate that ADCC mechanisms, with IgM as the primary effector molecule, appeared early in evolution.

Animals↗
PubMed1986

T cell receptor gene rearrangements in cells with natural killer activity in the mouse.

Cell-mediated recognition can operate at different levels of complexity and specificity based largely on the time of appearance of effector mechanisms during the course of evolution. Antigen-specific cytotoxic T lymphocytes require both T cell receptor genes and lectin-like cell adhesion molecules (LFA-1, LFA-2, lymphocyte function-associated) to initiate and maintain stable effector target cell conjugates. Natural killer (NK) cells, on the other hand, do not require expression of T cell receptor genes in the recognition and killing of tumor cells and virally infected cells. Adhesion is mediated by a family of glycoprotein molecules, of which the LFA-1 and LFA-2 molecules appear as the most likely candidates. NK-mediated cytolysis proceeds in the absence of MHC restriction, but nevertheless appears to be triggered by depressed levels of self MHC products on the cell surface of target cells. Finally, interleukin 2-dependent, cloned cell lines with NK-like cytotoxic activity should no longer be considered as bona-fide NK cells but rather reclassified as a subset of T cells which displays NK function.

Animals↗
PubMedDate not supplied

Sequence alignment of the G-protein coupled receptor superfamily.

The multitude of G-protein coupled receptor (GPR) superfamily cDNAs recently isolated has exceeded the number of receptor subtypes anticipated by pharmacological studies. Analysis of the sequence similarities and unique features of the members of this family is valuable for designing strategies to isolate related cDNAs, for developing hypotheses concerning substrate-ligand and receptor-effector interactions, and for understanding the evolution of these genes. We have compiled and aligned the 74 unique amino acid sequences published to date and review the present understanding of the structural motifs contributing to ligand binding and G-protein coupling.

Amino Acid Sequence↗
PubMed1990

Proteins as biological effectors.

This chapter presented an overview of the role of proteins as biological effectors. From a simplistic point of view, based solely on comparison of the structural diversity of immunoglobulins, blood coagulation proteins, gonadotropins, growth factors, and antiproteins, it could be concluded that the functional mechanisms of these protein families bear little or no relationship. Despite this enormous divergency in structure-function relationship, there are in fact elements of commonality in their effector roles arising as a direct consequence of the ability of these classes of protein effectors to act as exquisite examples of the processes of biorecognition. All these case histories, and the numerous other familial case studies of protein effectors which could have been employed to illustrate the different functional roles of proteins, owe their biological properties to their primordial protein antecedents which have traversed the harsh wilderness of evolution in biorecognition phenomena and survived to elicit specific effector roles. Dictated by underlying physicochemical constraints, deceived at times by the lulling tones of the siren entropy, and constantly vulnerable to the vagaries of other more pervasive forms of biological networking and information transfer encoded in the genes of virus and invading microorganisms, protein biorecognition in higher life forms, and particularly in mammals, represents the finely tuned molecular avenues for the genome to transfer its information to the next generation. The examples summarized in this chapter illustrate the complex, and in disease states imperfect, functional potential of proteins to be manifested in the jigsaw of biorecognition and be realized in the network of nature's biological effectors. Proteins thus represent a diverse range of effector molecules whose properties are totally dependent on their conformational or topographic status. The three-dimensional structure defines active sites on the molecule through which intermolecular interaction and biorecognition phenomena can occur. The cipher for this surface topography is, of course, coded in the primary amino acid sequence. Much experimental work is being directed in these and other laboratories at elucidating the principles governing the folding of unique peptide sequences into three-dimensional structures. Further advances in the theoretical understanding of the thermodynamics of protein folding as observed by x-ray crystallography, nuclear magnetic resonance and other spectroscopic techniques will greatly aid this quest. In addition, more comprehensive computer-aided algorithms for structure simulation, improved models of protein conformational behavior, and greater insight into the molecular forces which control sequence nucleation will also be required.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2026

Rapidly evolving aphid gall effector proteins exhibit saposin-like folds.

Many insects manipulate plants by injecting effector proteins. In one extreme example of this molecular "hijacking," Hormaphis cornu aphids inject bicycle proteins into Hamamelis virginiana, contributing to the development of novel organs called galls. Bicycle proteins share no amino acid sequence similarity with proteins of known function. Here, we report the crystal structures of two divergent bicycle proteins. Both proteins contain saposin-like folds: one with multiple disulfide bonds exhibits a swapped domain topology; the other has no disulfide bonds and possesses two distinct, tandem domains. To explore the structural evolution of bicycle proteins, we attempted to predict bicycle protein structures with Alphafold2 (AF2) and other deep learning programs. While AF2 did not recover the two experimental structures using existing databases, it succeeded when provided with multiple sequence alignments (MSAs) of protein sequences from newly sequenced closely related species. Using this approach, we generated 2,400 high-confidence bicycle protein predictions from seven aphid species. While all aphid bicycle proteins contain predicted saposin-like folds, they display a vast diversity of structural and physicochemical properties. While this diversity thwarts prediction of conserved functions encoded in structure, it suggests that bicycle proteins have evolved to target diverse plant processes and/or to evade plant immune surveillance. Our extension of AF2 with custom MSAs of proteins from closely related species provides a generalizable, powerful approach for predicting structures of rapidly evolving protein families.

Animals↗
PubMed1991

Sustained increases in cytosolic calcium during T lymphocyte allosensitization, proliferation, and acquisition of locomotor function.

Activation of resting T cells is accompanied by an increase in cytosolic calcium ([Ca2+]i). However, the role of [Ca2+]i in the effector function of allosensitized cells, and how this may affect the evolution of the allograft response is unknown. To evaluate this more directly, we determined [Ca2+]i in both unsensitized T cells (C57BL/6 murine thymocytes) and in allosensitized T cells derived from different days of a C57BL/6 anti-DBA/2J mixed leukocyte culture. To correlate potential changes in [Ca2+]i with concomitant development of T cell effector function, the [Ca2+]i, proliferation (3HTdR uptake), and random locomotion (in vitro modified Boyden chamber assay) of the same cells was assayed simultaneously. Allosensitized T cells exhibited higher (P less than 0.05) [Ca2+]i than unsensitized thymocytes on all days of culture tested. Further, there was a progressive rise in [Ca2+]i during the course of allosensitization. Con A stimulated an increase in [Ca2+]i over basal levels (P less than .05) for all cell types. A rise in [Ca2+]i preceded the onset of maximal allosensitized T cell proliferation (which peaked at day 7) and this continued to increase even after completion of DNA synthesis. In contrast, optimal T cell locomotion coincided with maximal [Ca2+]i, well after cell division had occurred. Prostaglandin E2, a known inhibitor of lymphocyte function, did not alter either basal or Con A-stimulated [Ca2+]i in thymocytes or MLC cells. These results indicate that [Ca2+]i signaling persists long after initial T lymphocyte alloactivation, and is maintained during DNA synthesis and acquisition of locomotor capacity. Furthermore, the inhibitory effects of PGE2 on allosensitized T lymphocyte function may be mediated by a calcium-independent mechanism.

Animals↗
PubMed2026

Effector loss and gain drives host range at a fitness cost.

Epidemic preparedness depends on tracking microbial evolution that drives shifts in ecological behaviors such as disease emergence. However, the genetic constraints mediating microbial emergence for generalist and specialist behaviors remain poorly described. Here, we addressed this question by combining comparative and functional genomics with phylogeny-based evolutionary analyses of the cereal pathogen Xanthomonas translucens. We show that a generalist X. translucens subgroup arose from a specialist ancestor, and the loss of a single effector gene, xopAL1, contributed to the generalist host expansion by promoting host jump from barley to wheat. Deleting barley-specialist X. translucens xopAL1 recapitulated the host jump to wheat and demonstrates risk across each globally distributed genetic lineage. However, this niche expansion via XopAL1 loss incurs a significant fitness cost to colonize barley. Moreover, the specialist lineage gained an additional effector gene, xopAJ, which enhanced virulence on barley while restricting oat infection, thereby reinforcing niche specialization. We further conducted transcriptomic analysis of wheat and determined that XopAL1 triggers a defense response that involves the reduction of photosynthetic processes. Our work provides an experimentally validated evolutionary framework to understand mechanisms of intergenera host jump. Overall, we demonstrate that single events of gene loss and gain shape ecological behaviors by creating a dynamic trade-off between niche breadth and specialization.

Triticum↗
PubMed2026

Precision Engineering of Evolution-Resilient Rice against Bacterial Blight.

The persistent conflict between rice and Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight, exemplifies a dynamic genetic arms race in agriculture. The cyclical deployment and erosion of major resistance (R) genes highlight the high adaptive potential of Xoo and the need for strategies that are durable rather than absolute. This review synthesizes a paradigm shift from reactive, single R-gene deployment toward proactive engineering of evolution-resilient resistance. We explore the molecular-genetic basis of Xoo adaptability, including TAL effector diversification, non-TAL virulence functions, genome variation, and immune suppression mechanisms. In response, we propose a framework for durable disease management with three connected components: precision disarmament through editing of susceptibility-gene effector-binding elements and executor/decoy designs; smart induction through targeted delivery and immune priming; and ecological fortification through protective microbiomes. We also discuss the limits, trade-offs, and field-validation requirements of these approaches. Integrating frontier technologies with evolutionary genetics, predictive genomics, and pathogen population dynamics can help develop rice varieties and deployment systems that are more difficult for Xoo populations to overcome.

CRISPR↗