Browsing by Person "Kube, Michael"

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Differential gene expression of Hymenoscyphus fraxineus grown on Fraxinus excelsior and F. mandshurica supplemented media
(2024) Zübert, Christina; Kube, Michael
Ash dieback is caused by the invasive fungal species Hymenoscyphus fraxineus and leads to the loss of the common ash ( Fraxineus excelsior ) in many areas. In contrast, the pathogen seems to colonize the local ash species Fraxinus mandshurica (Manchurian ash) symptom-free in its native environment East Asia. In order to gain insight into the differences in the substrate dependence of the pathogen, two H. fraxineus strains (1511 and 1431) were grown in media supplemented with leave material of F. excelsior or F. mandshurica and without supplement. A total of 95 and 916 genes were upregulated in media containing F. excelsior leaf material for strain 1431, compared to F. mandshurica and media without plant supplementation. The differential expression analysis of strain 1511 revealed 483 and 875 upregulated genes. Oxidative phosphorylation is highly upregulated in strain 1431 cultivated in F. excelsior- supplemented media indicating an active metabolism but probably also linked to the release of reactive oxygen species. In both strains during growth on F. excelsior , transcripts with similarity to genes of toxin biosynthetic pathways of other Ascomycota are enriched. In strain 1511, a gene cluster with similarity to depudecin cluster is upregulated in addition. For both strains, the upregulated genes, if grown in media supplemented with leaf material from F. excelsior, include a gene of the biosynthetic cluster of phytotoxin viridiol. The results suggest increased metabolic activity and toxin production in the presence of F. excelsior tissue compared to F. mandshurica.
Divergence within the taxon ‘Candidatus Phytoplasma asteris’ confirmed by comparative genome analysis of carrot strains
(2024) Toth, Rafael; Ilic, Anna-Marie; Huettel, Bruno; Duduk, Bojan; Kube, Michael
Phytoplasmas are linked to diseases in hundreds of economically important crops, including carrots. In carrots, phytoplasmosis is associated with leaf chlorosis and necrosis, coupled with inhibited root system development, ultimately leading to significant economic losses. During a field study conducted in Baden-Württemberg (Germany), two strains of the provisional taxon ‘Candidatus Phytoplasma asteris’ were identified within a carrot plot. For further analysis, strains M8 and M33 underwent shotgun sequencing, utilising single-molecule-real-time (SMRT) long-read sequencing and sequencing-by-synthesis (SBS) paired-end short-read sequencing techniques. Hybrid assemblies resulted in complete de novo assemblies of two genomes harboring circular chromosomes and two plasmids. Analyses, including average nucleotide identity and sequence comparisons of established marker genes, confirmed the phylogenetic divergence of ‘Ca. P. asteris’ and a different assignment of strains to the 16S rRNA subgroup I-A for M33 and I-B for M8. These groups exhibited unique features, encompassing virulence factors and genes, associated with the mobilome. In contrast, pan-genome analysis revealed a highly conserved gene set related to metabolism across these strains. This analysis of the Aster Yellows (AY) group reaffirms the perception of phytoplasmas as bacteria that have undergone extensive genome reduction during their co-evolution with the host and an increase of genome size by mobilome.
Genome comparison of ‘Candidatus Phytoplasma rubi’ with genomes of other 16SrV phytoplasmas highlights special group features
(2023) Böhm, Jan Werner; Duckeck, Dominik; Duduk, Bojan; Schneider, Bernd; Kube, Michael
Phytoplasmas are associated with important bacterial diseases, causing severe symptoms in agricultural and ornamental crops. ‘Candidatus Phytoplasma rubi’, associated with the Rubus stunt in raspberries (Rubus idaeus) and blackberries (Rubus subgenus Rubus), causes shortened internodes, elongated sepals, proliferation, phyllody, and virescence. The recently published genome of ‘Ca. P. rubi’ RS enabled a comprehensive genomic comparison to the complete genomes of 16SrV phytoplasmas, comprising strains of the flavescence dorée-associated phytoplasma CH and two ‘Candidatus Phytoplasma ziziphi’ strains. Besides the typical transporters and metabolic features of phytoplasmas, the phosphorolysis of sucrose and the utilization of the carboxylic acid L-lactate became apparent for the 16SrV-group. With respect to the effector repertoire and the encoded immunodominant membrane proteins involved in host colonization, the group revealed conserved features that comprise the variable membrane proteins A and B. However, SAP11- and SAP54 orthologs were limited to ‘Ca. P. rubi’ RS and ‘Ca. P. ziziphi’. Genome-sequence-based phylogenetic analysis supports the close relationship of these genomes relative to alder yellows phytoplasmas. The analyses supported the impact of the mobilome on phytoplasma evolution but also highlighted that there is the possibility of identifying phytoplasmas with a larger metabolic repertoire in the future.
The genome reduction excludes the ribosomal rescue system in acholeplasmataceae
(2022) Zübert, Christina; Ilic, Anna-Marie; Duduk, Bojan; Kube, Michael
The trans-translation process is a ribosomal rescue system for stalled ribosomes processing truncated mRNA. The genes ssrA and smpB fulfil the key functions in most bacteria, but some species have either lost these genes or the function of the ribosomal rescue system is taken over by other genes. To date, the ribosomal rescue system has not been analysed in detail for the Acholeplasmataceae. This family, in the Mollicutes class, comprises the genus Acholeplasma and the provisional taxon “Candidatus Phytoplasma”. Despite their monophyletic origin, the two clades can be separated by traits such as not representing primary pathogens for acholeplasmas versus being phytopathogenic for the majority of phytoplasmas. Both taxa share reduced genomes, but only phytoplasma genomes are characterised by a remarkable level of instability and reduction. Despite the general relevance of the ribosomal rescue system, information is lacking on coding, the genomic context and pseudogenisation of smpB and ssrA and their possible application as a phylogenetic marker. Herein, we provide a comprehensive analysis of the ribosomal rescue system in members of Acholeplasmataceae. The examined Acholeplasmataceae genomes encode a ribosomal rescue system, which depends on tmRNA encoded by ssrA acting in combination with its binding protein SmpB. Conserved gene synteny is evident for smpB, while ssrA shows a less conserved genomic context. Analysis of the tmRNA sequences highlights the variability of proteolysis tag sequences and short conserved sites at the 5′- and 3′-ends. Analyses of smpB provided no hints regarding the coding of pseudogenes, but they did suggest its application as a phylogenetic marker of Acholeplasmataceae – in accordance with 16S rDNA topology. Sequence variability of smpB provides sufficient information for species assignment and phylogenetic analysis.
The 16SrXII-P phytoplasma GOE is separated from other stolbur phytoplasmas by key genomic features
(2025) Toth, Rafael; Huettel, Bruno; Varrelmann, Mark; Kube, Michael; Kizheva, Yoana; Hristova, Petya
The syndrome “bassess richesses” is a vector-borne disease of sugar beet in Germany. The gammaproteobacterium ‘ Candidatus Arsenophonus phytopathogenicus’ causes reduced sugar content and biomass, growth abnormalities, and yellowing. Co-infection with the 16SrXII-P stolbur phytoplasmas often leads to more severe symptoms and a risk of complete economic loss. This yellowing agent of the Mollicutes class had not been described before, so its differences from other stolbur phytoplasmas remained unanswered. The genome of strain GOE was sequenced, providing a resource to analyze its characteristics. Phylogenetic position was revised, genome organization was compared, and functional reconstructions of metabolic and virulence factors were performed. Average nucleotide identity analysis indicates that GOE represents a new ‘ Ca. Phytoplasma’ species. Our results show that GOE is also distinct from other stolbur phytoplasmas in terms of smaller genome size and G+C content. Its reductive evolution is reflected in conserved membrane protein repertoire and minimal metabolism. The encoding of a riboflavin kinase indicates a lost pathway of phytoplasmas outside the groups 16SrXII and 16SrXIII. GOE shows a complete tra5 transposon harboring orthologs of SAP11, SAP54, and SAP05 effectors indicating an original phytoplasma pathogenicity island. Our results deepen the understanding of phytoplasma evolution and reaffirm the heterogeneity of stolbur phytoplasmas.