Epigenetics of the plant pathogen Zymoseptoria tritici

The genome of the fungal wheat pathogen Zymoseptoria tritici consists of thirteen essential chromosomes and several so-called dispensable chromosomes. These dispensable chromosomes encode only 6% of the protein coding genes of Z. tritici. To date no genes involved in pathogenicity are described on the dispensable chromosomes which can be lost after meiosis or mitotic cell division without any apparent effect on fitness. To investigate the underlying molecular basis of instability of the dispensable chromosomes, the epigenetic components of both the essential and dispensable chromosomes were characterized here. Chromatin immunoprecipitation and sequencing of DNA associated with the centromere specific histone (CenH3) was conducted to identify the centromeres of Z. tritici. It was shown that the centromeres of Z. tritici are small, sequence independent and lack any conserved motif. The centromeres are AT-rich, but not located in the most abundant AT-rich region of the chromosomes, and the centromeric organization is similar for both essential and dispensable chromosomes. To study centromere dynamic, parental and progeny strains derived from a meiotic cross were included in the study. The centromeres of these strains were shown to be conserved among Z. tritici strains. The deletion of the centromere of the dispensable chromosome 14 resulted in several strains were chromosome 14 was completely lost, while only a single strain was identified with a neocentromere on chromosome 14. The chromatin content of both types of chromosomes was also investigated. Three histone modifications specific for either euchromatin or heterochromatin were characterized. The essential chromosomes are enriched with euchromatin while the dispensable chromosomes are mainly heterochromatic. Several repeat rich regions with low gene density were also enriched with heterochromatin on the essential chromosomes. One particularly large region of 780 kb of the essential chromosome 7 was in addition found to be enriched with facultative heterochromatin. Genes in this region are silenced both during axenic and infectious growth. Based on the obtained results, it can be concluded that the difference between the essential and dispensable chromosomes cannot be associated with the centromeres. However, differences in the chromatin states is a main difference between the two types of chromosomes. To investigate the hemibiotrophic lifestyle switch in Z. tritici the epigenetic component of infectious growth was studied with a focus on RNA interference (RNAi). Five mutant strains of several proteins involved in the RNAi pathway were created. It could be demonstrated that Dicer and Argonaute genes play a role during the formation of asexual fruiting bodies called pycnidia. In contrast to the Dicer gene, the Argonaute genes show an unusual degree of sequence variation among Z. tritici strains. Collectively, the work presented here underlines the importance of epigenetics in both genome stability as well as pathogenicity in the fungal pathogen Z. tritici

Ago1 Affects the Virulence of the Fungal Plant Pathogen Zymoseptoria tritici

In host-pathogen interactions RNA interference (RNAi) has emerged as a pivotal mechanism to modify both, the immune responses of the host as well as the pathogenicity and virulence of the pathogen. In addition, in some fungi RNAi is also known to affect chromosome biology via its effect on chromatin conformation. Previous studies reported no effect of the RNAi machinery on the virulence of the fungal plant pathogen Zymoseptoria tritici however the role of RNAi is still poorly understood in this species. Herein, we elucidate whether the RNAi machinery is conserved within the genus Zymoseptoria. Moreover, we conduct functional analyses of Argonaute and Dicer-like proteins and test if the RNAi machinery affects chromosome stability. We show that the RNAi machinery is conserved among closely related Zymoseptoria species while an exceptional pattern of allelic diversity was possibly caused by introgression. The deletion of Ago1 reduced the ability of the fungus to produce asexual propagules in planta in a quantitative matter. Chromosome stability of the accessory chromosome of Z. tritici was not prominently affected by the RNAi machinery. These results indicate, in contrast to previous finding, a role of the RNAi pathway during host infection, but not in the stability of accessory chromosomes in Z. tritici

The hydrogenosomes of Psalteriomonas lanterna

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Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

Background: Supernumerary chromosomes have been found in many organisms. In fungi, these “accessory” or “dispensable” chromosomes are present at different frequencies in populations and are usually characterized by higher repetitive DNA content and lower gene density when compared to the core chromosomes. In the reference strain of the wheat pathogen, Zymoseptoria tritici, eight discrete accessory chromosomes have been found. So far, no functional role has been assigned to these chromosomes; however, they have existed as separate entities in the karyotypes of Zymoseptoria species over evolutionary time. In this study, we addressed what—if anything—distinguishes the chromatin of accessory chromosomes from core chromosomes. We used chromatin immunoprecipitation combined with high-throughput sequencing (“ChIP-seq”) of DNA associated with the centromere-specific histone H3, CENP-A (CenH3), to identify centromeric DNA, and ChIP-seq with antibodies against dimethylated H3K4, trimethylated H3K9 and trimethylated H3K27 to determine the relative distribution and proportion of euchromatin, obligate and facultative heterochromatin, respectively. Results: Centromeres of the eight accessory chromosomes have the same sequence composition and structure as centromeres of the 13 core chromosomes and they are of similar length. Unlike those of most other fungi, Z. tritici centromeres are not composed entirely of repetitive DNA; some centromeres contain only unique DNA sequences, and bona fide expressed genes are located in regions enriched with CenH3. By fluorescence microscopy, we showed that centromeres of Z. tritici do not cluster into a single chromocenter during interphase. We found dramatically higher enrichment of H3K9me3 and H3K27me3 on the accessory chromosomes, consistent with the twofold higher proportion of repetitive DNA and poorly transcribed genes. In contrast, no single histone modification tested here correlated with the distribution of centromeric nucleosomes. Conclusions: All centromeres are similar in length and composed of a mixture of unique and repeat DNA, and most contain actively transcribed genes. Centromeres, subtelomeric regions or telomere repeat length cannot account for the differences in transfer fidelity between core and accessory chromosomes, but accessory chromosomes are greatly enriched in nucleosomes with H3K27 trimethylation. Genes on accessory chromosomes appear to be silenced by trimethylation of H3K9 and H3K27.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central. The published article can be found at: http://www.epigeneticsandchromatin.com/. Supporting information available online at: http://www.epigeneticsandchromatin.com/content/8/1/41Keywords: Histone methylation, ChIP-seq, Zymoseptoria tritici (Mycosphaerella graminicola), Centromere, Accessory chromosome

Surgical resection and radiofrequency ablation initiate cancer in cytokeratin-19(+)- liver cells deficient for p53 and Rb

The long term prognosis of liver cancer patients remains unsatisfactory because of cancer recurrence after surgical interventions, particularly in patients with viral infections. Since hepatitis B and C viral proteins lead to inactivation of the tumor suppressors p53 and Retinoblastoma (Rb), we hypothesize that surgery in the context of p53/Rb inactivation initiate de novo tumorigenesis. We, therefore, generated transgenic mice with hepatocyte and cholangiocyte/liver progenitor cell (LPC)-specific deletion of p53 and Rb, by interbreeding conditional p53/Rb knockout mice with either Albumin-cre or Cytokeratin-19-cre transgenic mice. We show that liver cancer develops at the necrotic injury site after surgical resection or radiofrequency ablation in p53/Rb deficient livers. Cancer initiation occurs as a result of specific migration, expansion and transformation of cytokeratin-19+-liver (CK-19+) cells. At the injury site migrating CK-19+ cells formed small bile ducts and adjacent cells strongly expressed the transforming growth factor β (TGFβ). Isolated cytokeratin-19+ cells deficient for p53/Rb were resistant against hypoxia and TGFβ-mediated growth inhibition. CK-19+ specific deletion of p53/Rb verified that carcinomas at the injury site originates from cholangiocytes or liver progenitor cells. These findings suggest that human liver patients with hepatitis B and C viral infection or with mutations for p53 and Rb are at high risk to develop tumors at the surgical intervention site

The Oxytricha trifallax Mitochondrial Genome

The Oxytricha trifallax mitochondrial genome contains the largest sequenced ciliate mitochondrial chromosome (∼70 kb) plus a ∼5-kb linear plasmid bearing mitochondrial telomeres. We identify two new ciliate split genes (rps3 and nad2) as well as four new mitochondrial genes (ribosomal small subunit protein genes: rps- 2, 7, 8, 10), previously undetected in ciliates due to their extreme divergence. The increased size of the Oxytricha mitochondrial genome relative to other ciliates is primarily a consequence of terminal expansions, rather than the retention of ancestral mitochondrial genes. Successive segmental duplications, visible in one of the two Oxytricha mitochondrial subterminal regions, appear to have contributed to the genome expansion. Consistent with pseudogene formation and decay, the subtermini possess shorter, more loosely packed open reading frames than the remainder of the genome. The mitochondrial plasmid shares a 251-bp region with 82% identity to the mitochondrial chromosome, suggesting that it most likely integrated into the chromosome at least once. This region on the chromosome is also close to the end of the most terminal member of a series of duplications, hinting at a possible association between the plasmid and the duplications. The presence of mitochondrial telomeres on the mitochondrial plasmid suggests that such plasmids may be a vehicle for lateral transfer of telomeric sequences between mitochondrial genomes. We conjecture that the extreme divergence observed in ciliate mitochondrial genomes may be due, in part, to repeated invasions by relatively error-prone DNA polymerase-bearing mobile elements

Epigenetics of the plant pathogen Zymoseptoria tritici

The genome of the fungal wheat pathogen Zymoseptoria tritici consists of thirteen essential chromosomes and several so-called dispensable chromosomes. These dispensable chromosomes encode only 6% of the protein coding genes of Z. tritici. To date no genes involved in pathogenicity are described on the dispensable chromosomes which can be lost after meiosis or mitotic cell division without any apparent effect on fitness. To investigate the underlying molecular basis of instability of the dispensable chromosomes, the epigenetic components of both the essential and dispensable chromosomes were characterized here. Chromatin immunoprecipitation and sequencing of DNA associated with the centromere specific histone (CenH3) was conducted to identify the centromeres of Z. tritici. It was shown that the centromeres of Z. tritici are small, sequence independent and lack any conserved motif. The centromeres are AT-rich, but not located in the most abundant AT-rich region of the chromosomes, and the centromeric organization is similar for both essential and dispensable chromosomes. To study centromere dynamic, parental and progeny strains derived from a meiotic cross were included in the study. The centromeres of these strains were shown to be conserved among Z. tritici strains. The deletion of the centromere of the dispensable chromosome 14 resulted in several strains were chromosome 14 was completely lost, while only a single strain was identified with a neocentromere on chromosome 14. The chromatin content of both types of chromosomes was also investigated. Three histone modifications specific for either euchromatin or heterochromatin were characterized. The essential chromosomes are enriched with euchromatin while the dispensable chromosomes are mainly heterochromatic. Several repeat rich regions with low gene density were also enriched with heterochromatin on the essential chromosomes. One particularly large region of 780 kb of the essential chromosome 7 was in addition found to be enriched with facultative heterochromatin. Genes in this region are silenced both during axenic and infectious growth. Based on the obtained results, it can be concluded that the difference between the essential and dispensable chromosomes cannot be associated with the centromeres. However, differences in the chromatin states is a main difference between the two types of chromosomes. To investigate the hemibiotrophic lifestyle switch in Z. tritici the epigenetic component of infectious growth was studied with a focus on RNA interference (RNAi). Five mutant strains of several proteins involved in the RNAi pathway were created. It could be demonstrated that Dicer and Argonaute genes play a role during the formation of asexual fruiting bodies called pycnidia. In contrast to the Dicer gene, the Argonaute genes show an unusual degree of sequence variation among Z. tritici strains. Collectively, the work presented here underlines the importance of epigenetics in both genome stability as well as pathogenicity in the fungal pathogen Z. tritici