Books and chapters
Knogge, W. Diseases affecting barley: scald (Ed. Oliver R). Burleigh Dodds Series in Agricultural Science 183-215, (2018) ISBN: 9781786762160 DOI: 10.19103/as.2018.0039.10
Scald (leaf blotch), caused by the hemibiotrophic
pathogen Rhynchosporium commune, is one of the major diseases of barley
worldwide. Typical disease symptoms consist of necrotic areas on the
leaf blades. Yield losses are manifested as reduced kernel quality, size
and number per ear. This chapter reviews the origins, epidemiology and
other characteristic features of scald, and considers the agricultural
consequences of the pathogen’s biology. It then considers resistance
breeding programmes in which more than a dozen major resistance genes as
well as quantitative trait loci have been identified, and discusses
strategies to minimize the damage caused by the disease comprising
agricultural practices and different fungicides.
Penselin, D.; Münsterkötter, M.; Kirsten, S.; Felder, M.; Taudien, S.; Platzer, M.; Ashelford, K.; Paskiewicz, K. H.; Harrison, R. J.; Hughes, D. J.; Wolf, T.; Shelest, E.; Graap, J.; Hoffmann, J.; Wenzel, C.: Wöltje, N.; King, K. M.; Fitt, B. D. L.; Güldener, U.; Avrova, A.; Knogge, W. Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses BMC Genomics 17, 953, (2016) DOI: 10.1186/s12864-016-3299-5
BackgroundThe Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts.ResultsThe genomes of the different Rhynchosporium species were sequenced, assembled and annotated using ab initio gene predictors trained on several fungal genomes as well as on Rhynchosporium expressed sequence tags. Structures of the rDNA regions and genome-wide single nucleotide polymorphisms provided a hypothesis for intra-genus evolution. Homology screening detected core meiotic genes along with most genes crucial for sexual recombination in ascomycete fungi. In addition, a large number of cell wall-degrading enzymes that is characteristic for hemibiotrophic and necrotrophic fungi infecting monocotyledonous hosts were found. Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding for polyketide synthases and non-ribosomal peptide synthetases. Several of these genes are missing from the genome of the closest sequenced relative, the poplar pathogen Marssonina brunnea, and are possibly involved in adaptation to the grass hosts. Most importantly, six species-specific genes coding for protein effectors were identified in R. commune. Their deletion yielded mutants that grew more vigorously in planta than the wild type.ConclusionBoth cryptic sexuality and secondary metabolites may have contributed to host adaptation. Most importantly, however, the growth-retarding activity of the species-specific effectors suggests that host adaptation of R. commune aims at extending the biotrophic stage at the expense of the necrotrophic stage of pathogenesis. Like other apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host leaves relatively slowly without causing symptoms, reminiscent of the development of endophytic fungi. Rhynchosporium may therefore become an object for studying the mutualism-parasitism transition.
Siersleben, S.; Penselin, D.; Wenzel, C.; Albert, S.; Knogge, W. PFP1, a gene encoding an Epc-N domain-containing protein, is essential forpathogenicity of the barley pathogen Rhynchosporium commune. Eukaryot. Cell 13, 1026-1035, (2014) DOI: 10.1128/EC.00043-14
Scald caused by Rhynchosporium commune is an important foliar disease of barley. Insertion mutagenesis of R. commune generated a non-pathogenic fungal mutant, which carries the inserted plasmid in the upstream region of a gene named PFP1. The characteristic feature of the gene product is an Epc-N domain. This motif is also found in homologous proteins shown to be components of histone acetyltransferase (HAT) complexes of fungi and animals. Therefore, PFP1 is suggested to be the subunit of a HAT complex in R. commune with an essential role in the epigenetic control of fungal pathogenicity. Targeted PFP1 disruption also yielded non-pathogenic mutants, which showed wild-type like growth ex planta except for the occurrence of hyphal swellings. Complementation of the deletion mutants with the wild-type gene reestablished pathogenicity and suppressed the hyphal swellings. However, despite wild-type level PFP1 expression the complementation mutants did not reach wild-type level virulence. This indicates that the function of the protein complex and, thus, fungal virulence is influenced by a position-affected long-range control of PFP1 expression.
Hawkins, N.J.; Cools, H.J.; Sierotzki, H.; Shaw, M.W.; Knogge, W.; Kelly,
S.L.; Kelly, D.E.; Fraaije, B.A. Paralogue re-emergence: a novel, historically-contingent mechanism in the evolution of anti-microbial resistance. Mol Biol Evol 31, 1793-1802, (2014) DOI: 10.1093/molbev/msu134
Evolution of resistance to drugs and pesticides poses a serious threat to human health and agricultural production. CYP51 encodes the target site of azole fungicides, widely used clinically and in agriculture. Azole resistance can evolve due to point mutations or overexpression of CYP51 , and previous studies have shown that fungicide-resistant alleles have arisen by de novo mutation. Paralogs CYP51A and CYP51B are found in filamentous ascomycetes, but CYP51A has been lost from multiple lineages. Here, we show that in the barley pathogen Rhynchosporium commune, re-emergence of CYP51A constitutes a novel mechanism for the evolution of resistance to azoles. Pyrosequencing analysis of historical barley leaf samples from a unique long-term experiment from 1892 to 2008 indicates that the majority of the R.commune population lacked CYP51A until 1985, after which the frequency of CYP51A rapidly increased. Functional analysis demonstrates that CYP51A retains the same substrate as CYP51B , but with different transcriptional regulation. Phylogenetic analyses show that the origin of CYP51A far predates azole use, and newly sequenced Rhynchosporium genomes show CYP51A persisting in the R. commune lineage rather than being regained by ho rizontal gene transfer; therefore, CYP51A re-emergence provides an example of adaptation to novel compounds by selection from standing genetic variation.
Torriani, S.F.F.; Penselin, D.; Knogge, W.; Felder, M.; Taudien, S.;
Platzer, M.; McDonald, B.A.; Brunner, P.C. Comparative analysis of mitochondrial genomes from closely related Rhynchosporium species reveals extensive intron invasion Fungal Gen Biol 62, 34-42, (2014) DOI: 10.1016/j.fgb.2013.11.001
We sequenced and annotated the complete mitochondrial (mt) genomes of four closely related Rhynchosporium species that diverged ∼14,000–35,000 years ago. During this time frame, three of the mt genomes expanded significantly due to an invasion of introns into three genes (cox1, cox2, and nad5). The enlarged mt genomes contained ∼40% introns compared to 8.1% in uninvaded relatives. Many intron gains were accompanied by co-conversion of flanking exonic regions. The comparative analysis revealed a highly variable set of non-intronic, free-standing ORFs of unknown function (uORFs). This is consistent with a rapidly evolving accessory compartment in the mt genome of these closely related species. Only one free-standing uORF was shared among all mt genomes analyzed. This uORF had a mutation rate similar to the core mt protein-encoding genes, suggesting conservation of function among the species. The nucleotide composition of the core protein-encoding genes significantly differed from those of introns and uORFs. The mt mutation rate was 77 times higher than the nuclear mutation rate, indicating that the phylogeny inferred from mt genes may better resolve the phylogenetic relationships among closely related Rhynchosporium species than phylogenies inferred from nuclear genes.
Navarro-Quezada, A.; Schumann, N. & Quint, M. Plant F-Box protein evolution is determined by lineage-specific timing of major gene family expansion waves PLoS One 8, e68672, (2013) DOI: 10.1371/journal.pone.0068672
F-box proteins (FBPs) represent one of the largest and fastest evolving
gene/protein families in the plant kingdom. The FBP superfamily can be
divided in several subfamilies characterized by different C-terminal
protein-protein interaction domains that recruit targets for proteasomal
degradation. Hence, a clear picture of their phylogeny and molecular
evolution is of special interest for the general understanding of
evolutionary histories of multi-domain and/or large protein families in
plants. In an effort to further understand the molecular evolution of
F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana,
which carries a C-terminal F-box associated domain (FBA proteins)
shares evolutionary patterns and signatures of selection with other
FBPs. To address this question, we applied phylogenetic and molecular
evolution analyses in combination with the evaluation of transcriptional
profiles. Based on the 2219 FBA proteins we de novo identified
in 34 completely sequenced plant genomes, we compared their
evolutionary patterns to a previously analyzed large subfamily carrying
C-terminal kelch repeats. We found that these two large FBP subfamilies
generally tend to evolve by massive waves of duplication, followed by
sequence conservation of the F-box domain and sequence diversification
of the target recruiting domain. We conclude that the earlier in
evolutionary time a major wave of expansion occurred, the more
pronounced these selection signatures are. As a consequence, when
performing cross species comparisons among FBP subfamilies, significant
differences will be observed in the selective signatures of
protein-protein interaction domains. Depending on the species, the
investigated subfamilies comprise up to 45% of the complete superfamily,
indicating that other subfamilies possibly follow similar modes of
Kirsten, S.; Navarro-Quezada, A.; Penselin, D.; Wenzel, C.; Matern, A.; Leitner, A.; Baum, T.; Seiffert, U.; Knogge, W. Necrosis-Inducing Proteins of Rhynchosporium commune, Effectors in Quantitative Disease Resistance Mol Plant Microbe Interact 25, 1314-1325, (2012) DOI: 10.1094/MPMI-03-12-0065-R
The barley pathogen Rhynchosporium commune secretes necrosis-inducing proteins NIP1, NIP2, and NIP3. Expression analysis revealed that NIP1 transcripts appear to be present in fungal spores already, whereas NIP2 and NIP3 are synthesized after inoculation of host plants. To assess the contribution of the three effector proteins to disease development, deletion mutants were generated. The development of these fungal mutants on four barley cultivars was quantified in comparison with that of the parent wild-type strain and with two fungal strains failing to secrete an “active” NIP1 avirulence protein, using quantitative polymerase chain reaction as well as microscopic imaging after fungal green fluorescent protein tagging. The impact of the three deletions varied quantitatively depending on the host genotype, suggesting that the activities of the fungal effectors add up to produce stronger growth patterns and symptom development. Alternatively, recognition events of differing intensities may be converted into defense gene expression in a quantitative manner.
Avrova, A.; Knogge, W. Rhynchosporium commune: a persistent threat to barley cultivation Mol Plant Pathol 13, 986-997, (2012) DOI: 10.1111/j.1364-3703.2012.00811.x
Rhynchosporium commune is a haploid fungus causing scald or leaf blotch on barley, other Hordeum spp. and Bromus diandrus.TaxonomyRhynchosporium
commune is an anamorphic Ascomycete closely related to the teleomorph
Helotiales genera Oculimacula and Pyrenopeziza.Disease symptomsRhynchosporium
commune causes scald‐like lesions on leaves, leaf sheaths and ears.
Early symptoms are generally pale grey oval lesions. With time, the
lesions acquire a dark brown margin with the centre of the lesion
remaining pale green or pale brown. Lesions often merge to form large
areas around which leaf yellowing is common. Infection frequently occurs
in the leaf axil, which can lead to chlorosis and eventual death of the
leaf.Life cycleRhynchosporium commune is seed borne, but the
importance of this phase of the disease is not fully understood. Debris
from previous crops and volunteers, infected from the stubble from
previous crops, are considered to be the most important sources of the
disease. Autumn‐sown crops can become infected very soon after sowing.
Secondary spread of disease occurs mainly through splash dispersal of
conidia from infected leaves. Rainfall at the stem extension growth
stage is the major environmental factor in epidemic development.Detection and quantificationRhynchosporium
commune produces unique beak‐shaped, one‐septate spores both on leaves
and in culture. The development of a specific polymerase chain reaction
(PCR) and, more recently, quantitative PCR (qPCR) has allowed the
identification of asymptomatic infection in seeds and during the growing
season.Disease controlThe main measure for the control of
R. commune is the use of fungicides with different modes of action, in
combination with the use of resistant cultivars. However, this is
constantly under review because of the ability of the pathogen to adapt
to host plant resistance and to develop fungicide resistance.
Horbach, R.; Navarro-Quesada, A. R.; Knogge, W.; Deising, H. B. When and how to kill a plant cell: Infection strategies of plant pathogenic fungi. J Plant Physiol 168, 51-62, (2011) DOI: 10.1016/j.jplph.2010.06.014
Fungi cause severe diseases on a broad range of
crop and ornamental plants, leading to significant economical losses.
Plant pathogenic fungi exhibit a huge variability in their mode of
infection, differentiation and function of infection structures and
nutritional strategy. In this review, advances in understanding
mechanisms of biotrophy, necrotrophy and hemibiotrophic lifestyles are
described. Special emphasis is given to the biotrophy-necrotrophy switch
of hemibiotrophic pathogens, and to biosynthesis, chemical diversity
and mode of action of various fungal toxins produced during the
Baum, T.; Navarro-Quezada, A.; Knogge, W.; Douchkov, D.; Schweizer, P.; Seiffert, U. HyphArea—Automated analysis of spatiotemporal fungal patterns J Plant Physiol 168, 72-78, (2011) DOI: 10.1016/j.jplph.2010.08.004
In phytopathology quantitative measurements are
rarely used to assess crop plant disease symptoms. Instead, a
qualitative valuation by eye is often the method of choice. In order to
close the gap between subjective human inspection and objective
quantitative results, the development of an automated analysis system
that is capable of recognizing and characterizing the growth patterns of
fungal hyphae in micrograph images was developed. This system should
enable the efficient screening of different host–pathogen combinations
(e.g., barley—Blumeria graminis, barley—Rhynchosporium secalis) using
different microscopy technologies (e.g., bright field, fluorescence). An
image segmentation algorithm was developed for gray-scale image data
that achieved good results with several microscope imaging protocols.
Furthermore, adaptability towards different host–pathogen systems was
obtained by using a classification that is based on a genetic algorithm.
The developed software system was named HyphArea, since the
quantification of the area covered by a hyphal colony is the basic task
and prerequisite for all further morphological and statistical analyses
in this context. By means of a typical use case the utilization and
basic properties of HyphArea could be demonstrated. It was possible to
detect statistically significant differences between the growth of an R.
secalis wild-type strain and a virulence mutant.