Biology subjects

Croll, D.

Publications and source records attributed to Croll, D..

7 recordsLinked to original sources

bioRxiv2018

The monothiol glutaredoxin Grx4 interacts with the Cryptococcus iron regulator Cir1 and regulates iron homeostasis and virulence in the Cryptococcus neoformans

The acquisition of iron and the maintenance of iron homeostasis are important aspects of the virulence in the pathogenic fungus Cryptococcus neoformans. In this study, we identified the monothiol glutaredoxin Grx4 as a binding partner of Cir1, a master regulator of iron-responsive genes and virulence factor elaboration in C. neoformans. Monothiol glutaredoxins are important regulators of iron homeostasis because of their conserved roles in [2Fe-2S] cluster sensing and trafficking. We confirmed that Grx4 binds Cir1 and demonstrated that iron repletion promotes the relocalization of Grx4 from the nucleus to the cytoplasm. Nuclear retention is partially dependent on Cir1 and also influenced by treatment with the proteasome inhibitor bortezomib. Cir1 remains in the nucleus in both iron replete and iron limiting conditions. We also found that a grx4{Delta} mutant displayed iron-related phenotypes similar to those of a cir1{Delta} mutant, including poor growth upon iron deprivation. Importantly, a grx4{Delta} mutant was avirulent in mice, a phenotype consistent with observed defects in the key virulence determinants, capsule and melanin, and poor growth at 37{degrees}C. A comparative transcriptome analysis of a grx4{Delta} mutant and the WT strain in low iron and iron-replete conditions confirmed a central role for Grx4 in iron homeostasis. Dysregulation of iron-related metabolism was consistent with grx4{Delta} mutant phenotypes related to oxidative stress, mitochondrial function, and DNA repair. Overall, the phenotypes of the grx4{Delta} mutant and the RNA-Seq analysis support the hypothesis that Grx4 functions as a sensor of iron levels, in part through an interaction with Cir1, to extensively regulate iron homeostasis and contribute to virulence.

microbiology↗

bioRxiv2018

The MoT3 assay does not distinguish between Magnaporthe oryzae wheat and rice blast isolates from Bangladesh

The blast fungus Magnaporthe oryzae is comprised of lineages that exhibit varying degrees of specificity on about 50 grass hosts, including rice, wheat and barley. Reliable diagnostic tools are essential given that the pathogen has a propensity to jump to new hosts and spread to new geographic regions. Of particular concern is wheat blast, which has suddenly appeared in Bangladesh in 2016 before spreading to neighboring India. In these Asian countries, wheat blast strains are now co-occurring with the destructive rice blast pathogen raising the possibility of genetic exchange between these destructive pathogens. We assessed the recently described MoT3 diagnostic assay and found that it did not distinguish between wheat and rice blast isolates from Bangladesh. The assay is based on primers matching the WB12 sequence corresponding to a fragment of the M. oryzae MGG_02337 gene annotated as a short chain dehydrogenase. These primers could not reliably distinguish between wheat and rice blast isolates from Bangladesh based on DNA amplification experiments performed in separate laboratories in Bangladesh and in the UK. In addition, comparative genomics of the WB12 sequence revealed a complex underlying genetic structure with related sequences across M. oryzae strains and in both rice and wheat blast isolates. We, therefore, caution against the indiscriminate use of this assay to identify wheat blast.

plant biology↗

bioRxiv2018

Transposable element insertions shape gene regulation and melanin production in a fungal pathogen

Background\n\nVariation in gene expression contributes to phenotypic diversity within species and adaptation. However, very few cases of adaptive regulatory changes have been reported and the mechanisms underlying variation in gene expression remain largely unexplored. Fungal pathogen genomes are highly plastic and harbour numerous insertions of transposable elements, which can potentially contribute to gene expression regulation. In this work we elucidated how transposable elements contribute to variation of melanin accumulation, a quantitative adaptive trait of fungal pathogens that is involved in survival under stress conditions.\n\nResults\n\nWe demonstrated that differential transcriptional regulation of the gene encoding the transcription factor Zmr1, which controls expression of the genes in the melanin biosynthetic gene cluster, is responsible for variation in melanin accumulation in the fungal plant pathogen Zymoseptoria tritici. We show that differences in melanin levels between two strains of Z. tritici are due to two levels of transcriptional regulation: 1) variation in the promoter sequence of Zmr1, and 2) an insertion of transposable elements upstream of the Zmr1 promoter. Remarkably, independent insertions of transposable elements upstream of Zmr1 occurred in 9% of Z. tritici strains from around the world and negatively regulated Zmr1 expression, contributing to melanin accumulation variation.\n\nConclusions\n\nOur studies demonstrate that different layers of transcriptional control fine-tune the synthesis of melanin. These regulatory mechanisms potentially evolved to balance the fitness costs associated with melanin production against its positive contribution to survival in stressful environments.

molecular biology↗

bioRxiv2018

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

O_LICultivar-strain specificity in the wheat-Zymoseptoria tritici pathosystem determines the infection outcome and is controlled by resistance genes on the host side, of which many have been identified. However, on the pathogen side, the molecular determinants of specificity are largely unknown.\nC_LIO_LIWe used genetic mapping, targeted gene disruption and allele swapping to characterize the recognition of the new avirulence factor Avr3D1. We then combined population genetic and comparative genomic analyses to estimate the evolutionary trajectory of Avr3D1.\nC_LIO_LIAvr3D1 is specifically recognized by cultivars harboring the resistance gene Stb7 and triggers a strong defence response without preventing pathogen infection and reproduction. Avr3D1 resides in a cluster of putative effector genes located in a region populated by independent transposable element insertions. The gene is present in all 132 investigated strains and is highly polymorphic, with a total of 30 different protein variants. We demonstrated that certain amino acid mutations in Avr3D1 led to evasion of recognition.\nC_LIO_LIThese results demonstrate that quantitative resistance and gene-for-gene interactions are not mutually exclusive per se. Location of avirulence genes in highly plastic genomic regions likely facilitates accelerated evolution that enables escape from recognition by resistance proteins.\nC_LI

plant biology↗

bioRxiv2017

Genome-wide detection of genes under positive selection in worldwide populations of the barley scald pathogen

The coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect a specific host. Hence, heterogeneity in the host genotypes and abiotic factors leads to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. We analyzed global field populations of Rhynchosporium commune, the pathogen causing barley scald disease, to identify candidate genes for local adaptation. Whole genome sequencing data generated for 125 isolates showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded proteins with functions related to both biotic and abiotic stresses. We found that selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.

genomics↗

bioRxiv2017

Meiosis leads to pervasive segregation distortion and copy-number variation in accessory chromosomes of the wheat pathogen Zymoseptoria tritici

Meiosis is one of the most conserved molecular processes in eukaryotes. The fidelity of pairing and segregation of homologous chromosomes has a major impact on the proper transmission of genetic information. Aberrant chromosomal transmission can have major phenotypic consequences, yet the mechanisms are poorly understood. Fungi are excellent models to investigate processes of chromosomal transmission, because many species have highly polymorphic genomes that include accessory chromosomes. Inheritance of accessory chromosomes is often unstable and chromosomal losses have little impact on fitness. We analyzed chromosomal inheritance in 477 progeny coming from two crosses of the fungal wheat pathogen Zymoseptoria tritici. For this, we developed a high-throughput screening method based on restriction site associated DNA sequencing (RAD-seq) that generated dense coverage of genetic markers along each chromosome. We identified rare instances of chromosomal duplications (disomy) in core chromosomes. Accessory chromosomes showed high overall frequencies of disomy. Chromosomal rearrangements were found exclusively on accessory chromosomes and were more frequent than disomy. Accessory chromosomes present in only one of the parents in an analyzed cross were inherited at significantly higher rates than the expected 1:1 segregation ratio. Both the chromosome and the parental background had significant impacts on the rates of disomy, losses, rearrangements and segregation distortion. We found that chromosomes with higher sequence similarity and lower repeat content were inherited more faithfully. The large number of rearranged progeny chromosomes identified in this species will enable detailed analyses of the mechanisms underlying chromosomal rearrangement.

evolutionary biology↗

bioRxiv2017

The wheat blast pathogen Pyricularia graminis-tritici has complex origins and a disease cycle spanning multiple grass hosts

The wheat blast disease has been a serious constraint for wheat production in Latin America since the late 1980s. We used a population genomics analysis including 95 genome sequences of the wheat blast pathogen Pyricularia graminis-tritici (Pygt) and other Pyricularia species to show that Pygt is a distinct, highly diverse pathogen species with a broad host range. We assayed 11 neutral SSR loci in 526 Pygt isolates sampled from wheat and other grasses distributed across the wheat-growing region of Brazil to estimate gene flow, assess the importance of sexual reproduction, and compare the genetic structures of Pygt populations infecting wheat and nearby grasses. Our results suggest a mixed reproductive system that includes sexual recombination as well as high levels of gene flow among regions, including evidence for higher gene flow from grass-infecting populations and into wheat-infecting populations than vice versa. The most common virulence groups were shared between the grass- and wheat-infecting Pygt populations, providing additional evidence for movement of Pygt between wheat fields and nearby grasses. Analyses of fruiting body formation found that proto-perithecia and perithecia developed on senescing stems of wheat and other grass hosts, suggesting that sexual reproduction occurs mainly during the saprotrophic phase of the disease cycle on dead residues. Phalaris canariensis (canarygrass) supported the fullest development of perithecia, suggesting it is a promising candidate for identifying the teleomorph in the field. Based on these findings, we formulated a more detailed disease cycle for wheat blast that includes an important role for grasses growing near wheat fields. Our findings strongly suggest that widely grown pasture grasses function as a major reservoir of wheat blast inoculum and provide a temporal and spatial bridge that connects wheat fields across Brazil.\n\nAuthor summaryAfter the first wheat blast epidemic occurred in 1985 in Parana, Brazil, the disease spread to Bolivia, Argentina, and Paraguay, and was introduced into Bangladesh in 2016 followed by India in 2017. Wheat blast is caused by Pyricularia graminis-tritici (Pygt), a highly diverse pathogen species related to the rice blast fungus P. oryzae, but with an independent origin and a broader host range. We conducted a large scale contemporary sampling of Pygt from symptomatic wheat and other grass species across Brazil and analyzed the genetic structure of Pygt populations. Pygt populations on both wheat and other grasses had high genotypic and virulence diversity, a genetic structure consistent with a mixed reproductive system that includes regular cycles of recombination. The pathogen formed sexual fruiting structures (perithecia) on senescing stems of wheat and other grasses. Historical migration analyses indicated that the majority of gene flow has been from Pygt populations on other grasses and into the Pygt population infecting wheat, consistent with the hypothesis that Pygt originated on other grasses before becoming a wheat pathogen. We found that the Pygt populations infecting wheat were indistinguishable from the Pygt populations infecting other grass species, including signal grass (Urochloa brizantha). Because U. brizantha is a widely grown grass pasture often found next to wheat fields, we propose that it functions as reservoir of Pygt inoculum that provides a temporal and spatial bridge that connects wheat fields in Brazil.

plant biology↗