2025
Jose, Jisna; Teutloff, Erik; Mayer, Teresa; Naseem, Simrat; Barth, Emanuel; Halitschke, Rayko; Marz, Manja; Agler, Matthew T.
Immunity and bacterial recruitment in plant leaves are parallel processes that together shape sensitivity to temperature stress Journal Article
In: bioRxiv, 2025.
Abstract | Links | BibTeX | Tags: bacteria, evolution, fungi, metagenomics
@article{nokey_76,
title = {Immunity and bacterial recruitment in plant leaves are parallel processes that together shape sensitivity to temperature stress},
author = {Jisna Jose and Erik Teutloff and Teresa Mayer and Simrat Naseem and Emanuel Barth and Rayko Halitschke and Manja Marz and Matthew T. Agler},
doi = {10.1101/2024.06.10.598336},
year = {2025},
date = {2025-04-25},
journal = {bioRxiv},
abstract = {Rising global temperatures necessitate developing resilient crops with better adaptability to changing climates. Under elevated temperatures, plant immunity is downregulated, increasing risk of foliar pathogen attack. Manipulating plant defense hormones is one way to mitigate this detrimental effect. However, it is unclear how plant immunity interacts with plant microbiome assembly and how temperature will thus affect overall plant health and stability. In this study, we compared two Arabidopsis thaliana genotypes that feature divergent strategies for recruitment of commensal bacteria from natural soil. NG2, an A. thaliana ecotype we collected from Jena, Germany, was grown in its native soil and compared to CLLF, a genotype that recruits higher bacterial loads and higher bacterial diversity but without any dysbiotic phenotype. CLLF hyperaccumulates salicylic acid (SA) and jasmonates, has constitutively upregulated innate defenses, and shows increased resistance to necrotrophic fungal and hemi-biotrophic bacterial pathogens, indicating that pathogen immunity and non-pathogen recruitment function in parallel. Some of its leaf bacteria can utlize SA as a carbon source, suggesting that immunity and recruitment may even be linked by chemical hormones. CLLF exhibits high tolerance to heat stress in comparison to the NG2, with SA-associated defense processes remaining active under heat. Synthetic community (SynCom) experiments revealed that when the taxonomic diversity of bacteria available to CLLF is artificially reduced, resilience to heat stress is compromised, leading to dysbiosis. However, this dysbiosis does not occur in CLLF with a full SynCom or in the NG2 with any SynCom. These findings suggest that the downregulation of defenses in response to heat may contribute to the avoidance of dysbiosis caused by certain leaf bacteria, while full bacteriome taxonomic diversity can help maintain balance.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {bacteria, evolution, fungi, metagenomics},
pubstate = {published},
tppubtype = {article}
}
Rising global temperatures necessitate developing resilient crops with better adaptability to changing climates. Under elevated temperatures, plant immunity is downregulated, increasing risk of foliar pathogen attack. Manipulating plant defense hormones is one way to mitigate this detrimental effect. However, it is unclear how plant immunity interacts with plant microbiome assembly and how temperature will thus affect overall plant health and stability. In this study, we compared two Arabidopsis thaliana genotypes that feature divergent strategies for recruitment of commensal bacteria from natural soil. NG2, an A. thaliana ecotype we collected from Jena, Germany, was grown in its native soil and compared to CLLF, a genotype that recruits higher bacterial loads and higher bacterial diversity but without any dysbiotic phenotype. CLLF hyperaccumulates salicylic acid (SA) and jasmonates, has constitutively upregulated innate defenses, and shows increased resistance to necrotrophic fungal and hemi-biotrophic bacterial pathogens, indicating that pathogen immunity and non-pathogen recruitment function in parallel. Some of its leaf bacteria can utlize SA as a carbon source, suggesting that immunity and recruitment may even be linked by chemical hormones. CLLF exhibits high tolerance to heat stress in comparison to the NG2, with SA-associated defense processes remaining active under heat. Synthetic community (SynCom) experiments revealed that when the taxonomic diversity of bacteria available to CLLF is artificially reduced, resilience to heat stress is compromised, leading to dysbiosis. However, this dysbiosis does not occur in CLLF with a full SynCom or in the NG2 with any SynCom. These findings suggest that the downregulation of defenses in response to heat may contribute to the avoidance of dysbiosis caused by certain leaf bacteria, while full bacteriome taxonomic diversity can help maintain balance.Competing Interest StatementThe authors have declared no competing interest.
Oktay, Ceren; Shiko, Glendis; Liebl, Maximilian; Feistel, Felix; Mußbach, Sarah; Körber, Karl Ludwig; Barth, Emanuel; Huber, Ludwig; Antony, Anna; Oelmüller, Ralf; Reichelt, Michael; Ossetek, Kilian; Müller, Christoph; Furch, Alexandra C. U.; Klein, Jan
Arabidopsis thaliana accumulates dehydroepiandrosterone after infection with phytopathogenic fungi – effects on plants and fungi Journal Article
In: Plant Physiology and Biochemistry, 2025.
Abstract | Links | BibTeX | Tags: fungi, RNA / transcriptomics
@article{nokey,
title = {\textit{Arabidopsis thaliana} accumulates dehydroepiandrosterone after infection with phytopathogenic fungi – effects on plants and fungi},
author = {Ceren Oktay and Glendis Shiko and Maximilian Liebl and Felix Feistel and Sarah Mußbach and Karl Ludwig Körber and Emanuel Barth and Ludwig Huber and Anna Antony and Ralf Oelmüller and Michael Reichelt and Kilian Ossetek and Christoph Müller and Alexandra C.U. Furch and Jan Klein},
doi = {10.1016/j.plaphy.2025.109570},
year = {2025},
date = {2025-01-28},
urldate = {2025-01-28},
journal = {Plant Physiology and Biochemistry},
abstract = {Progestogens and androgens have been found in many plants, but little is known about their physiological function. We used a previously established UPLC-ESI-MS/MS method to analyze progestogen and androgen profiles in fungal infections. Here we show that dehydroepiandrosterone (DHEA), a C19 steroid, specifically accumulates in shoots of Arabidopsis thaliana (L.) HEYNH. infected with Alternaria brassicicola (SCHWEIN). Elevated DHEA levels in plants seem not to be product of fungal sterol/steroid precursor activity, but an intrinsic plant response to the infection. DHEA was applied exogenously to analyze the effects of the androgen on development and gene expression in A. thaliana. Our findings reveal that DHEA treatment downregulates membrane-associated, salicylic acid and abscisic acid-regulated, as well as stress-responsive genes. Notably, DHEA does not inhibit the isoprenoid or post-lanosterol pathway of the ergosterol biosynthesis. Moreover, A. brassicicola was also treated with DHEA to analyze the growth, sterol pattern and membrane-integrity. Our data suggest that DHEA enhances the permeability of plant and fungal biomembranes. We propose that DHEA accumulation is a plant defense response which reduces fungal growth in plant tissues.},
keywords = {fungi, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
Progestogens and androgens have been found in many plants, but little is known about their physiological function. We used a previously established UPLC-ESI-MS/MS method to analyze progestogen and androgen profiles in fungal infections. Here we show that dehydroepiandrosterone (DHEA), a C19 steroid, specifically accumulates in shoots of Arabidopsis thaliana (L.) HEYNH. infected with Alternaria brassicicola (SCHWEIN). Elevated DHEA levels in plants seem not to be product of fungal sterol/steroid precursor activity, but an intrinsic plant response to the infection. DHEA was applied exogenously to analyze the effects of the androgen on development and gene expression in A. thaliana. Our findings reveal that DHEA treatment downregulates membrane-associated, salicylic acid and abscisic acid-regulated, as well as stress-responsive genes. Notably, DHEA does not inhibit the isoprenoid or post-lanosterol pathway of the ergosterol biosynthesis. Moreover, A. brassicicola was also treated with DHEA to analyze the growth, sterol pattern and membrane-integrity. Our data suggest that DHEA enhances the permeability of plant and fungal biomembranes. We propose that DHEA accumulation is a plant defense response which reduces fungal growth in plant tissues.
Ornelas-Eusebio, Erika; Vorimore, Fabien; Aaziz, Rachid; Mandola, Maria-Lucia; Rizzo, Francesca; Marchino, Monica; Nogarol, Chiara; Risco-Castillo, Veronica; Zanella, Gina; Schnee, Christiane; Sachse, Konrad; Laroucau, Karine
Trichosporon asahii: A Potential Growth Promoter for C. gallinacea? Implications for Chlamydial Infections and Cell Culture Journal Article
In: Microorganisms, vol. 13, no. 2, 2025.
Abstract | Links | BibTeX | Tags: bacteria, fungi, metagenomics
@article{nokey_75,
title = {\textit{Trichosporon asahii}: A Potential Growth Promoter for \textit{C. gallinacea}? Implications for Chlamydial Infections and Cell Culture},
author = {Erika Ornelas-Eusebio and Fabien Vorimore and Rachid Aaziz and Maria-Lucia Mandola and Francesca Rizzo and Monica Marchino and Chiara Nogarol and Veronica Risco-Castillo and Gina Zanella and Christiane Schnee and Konrad Sachse and Karine Laroucau},
doi = {10.3390/microorganisms13020288},
year = {2025},
date = {2025-01-27},
urldate = {2025-01-27},
journal = {Microorganisms},
volume = {13},
number = {2},
abstract = {The cultivation of Chlamydia gallinacea, a recently identified species, is challenging due to the lack of an optimized protocol. In this study, several infection protocols were tested, including different cell lines, incubation temperatures, centrifugation methods and culture media. However, none were successful in field samples. The only exception was a chance co-culture with Trichosporon asahii, a microorganism commonly found in the chicken gut. This suggests that current in vitro methods may not be optimized for this species and that host-associated microorganisms may influence the in vivo growth of C. gallinacea, which is typically found in the chicken gut. These findings raise new questions and highlight the need for further investigation of microbial interactions within the host, particularly to understand their role in the proliferation of chlamydial species.},
keywords = {bacteria, fungi, metagenomics},
pubstate = {published},
tppubtype = {article}
}
The cultivation of Chlamydia gallinacea, a recently identified species, is challenging due to the lack of an optimized protocol. In this study, several infection protocols were tested, including different cell lines, incubation temperatures, centrifugation methods and culture media. However, none were successful in field samples. The only exception was a chance co-culture with Trichosporon asahii, a microorganism commonly found in the chicken gut. This suggests that current in vitro methods may not be optimized for this species and that host-associated microorganisms may influence the in vivo growth of C. gallinacea, which is typically found in the chicken gut. These findings raise new questions and highlight the need for further investigation of microbial interactions within the host, particularly to understand their role in the proliferation of chlamydial species.
2024
Jose, Jisna; Teutloff, Erik; Naseem, Simrat; Barth, Emanuel; Halitschke, Rayko; Marz, Manja; Agler, Matthew T.
Immunity and bacterial recruitment in plant leaves are parallel processes whose link shapes sensitivity to temperature stress Journal Article
In: bioRxiv, 2024.
Abstract | Links | BibTeX | Tags: bacteria, evolution, fungi, RNA / transcriptomics
@article{nokey,
title = {Immunity and bacterial recruitment in plant leaves are parallel processes whose link shapes sensitivity to temperature stress},
author = {Jisna Jose and Erik Teutloff and Simrat Naseem and Emanuel Barth and Rayko Halitschke and Manja Marz and Matthew T. Agler},
doi = {10.1101/2024.06.10.598336},
year = {2024},
date = {2024-06-10},
journal = {bioRxiv},
abstract = {Rising global temperatures necessitate developing climate-resilient crops with better adaptability to changing climates. Under elevated temperatures, plant immunity is downregulated, putting them at risk of foliar pathogen attack. Manipulating plant defense hormones is one way to mitigate this detrimental effect. However, it is unclear how plant immunity interacts with plant microbiome assembly and how temperature will thus affect overall plant health and stability. We used chemical mutagenesis to identify a phenotypically healthy genotype of A. thaliana, “CLLF”, that compared to the wild type naturally recruits an altered leaf bacteriome, including unusually high bacteria loads. Simultaneously, CLLF hyperaccumulates salicylic acid (SA) and jasmonates, has constitutively upregulated systemic and innate defenses, and has increased resistance to necrotrophic fungal and hemi-biotrophic bacterial pathogens, indicating that pathogen immunity and non-pathogen recruitment function in parallel. Growth of specific non-pathogenic leaf bacteria on SA as a carbon source suggests the same hormones may even link the two processes. CLLF also showed high tolerance to heat stress in comparison to the wild type, but SA-associated defense processes are not downregulated under heat. Synthetic community (SynCom) experiments showed that when the taxonomic diversity of bacteria available to CLLF is artificially reduced, resilience to heat stress is compromised, leading to dysbiosis, but this does not occur with the full SynCom or in the wild type with any SynCom. Thus, the downregulation of defenses in response to heat may contribute to avoidance of dysbiosis caused by some leaf bacteria, but full bacteriome taxonomic diversity can restore balance.
Significance Statement Plants are living ecosystems colonized by diverse microorganisms who strongly shape host health. Understanding how balance arises in host-associated microbiomes is a key step to understanding how to preserve, manage and possibly optimize these complex ecosystems, especially in a changing climate. Using a random mutagenesis approach in a natural A. thaliana ecotype, we find that constitutively upregulated defenses are associated with both tolerance to (a)biotic threats and healthy recruitment of leaf bacteria, very likely in a direct manner. Thus, immunity and bacterial recruitment in leaves operate in parallel. Synthetic community experiments show further that this link plays important roles in shaping plant resilience to heat stress, an important consideration in developing plants more stable to climate change.},
keywords = {bacteria, evolution, fungi, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
Rising global temperatures necessitate developing climate-resilient crops with better adaptability to changing climates. Under elevated temperatures, plant immunity is downregulated, putting them at risk of foliar pathogen attack. Manipulating plant defense hormones is one way to mitigate this detrimental effect. However, it is unclear how plant immunity interacts with plant microbiome assembly and how temperature will thus affect overall plant health and stability. We used chemical mutagenesis to identify a phenotypically healthy genotype of A. thaliana, “CLLF”, that compared to the wild type naturally recruits an altered leaf bacteriome, including unusually high bacteria loads. Simultaneously, CLLF hyperaccumulates salicylic acid (SA) and jasmonates, has constitutively upregulated systemic and innate defenses, and has increased resistance to necrotrophic fungal and hemi-biotrophic bacterial pathogens, indicating that pathogen immunity and non-pathogen recruitment function in parallel. Growth of specific non-pathogenic leaf bacteria on SA as a carbon source suggests the same hormones may even link the two processes. CLLF also showed high tolerance to heat stress in comparison to the wild type, but SA-associated defense processes are not downregulated under heat. Synthetic community (SynCom) experiments showed that when the taxonomic diversity of bacteria available to CLLF is artificially reduced, resilience to heat stress is compromised, leading to dysbiosis, but this does not occur with the full SynCom or in the wild type with any SynCom. Thus, the downregulation of defenses in response to heat may contribute to avoidance of dysbiosis caused by some leaf bacteria, but full bacteriome taxonomic diversity can restore balance.
Significance Statement Plants are living ecosystems colonized by diverse microorganisms who strongly shape host health. Understanding how balance arises in host-associated microbiomes is a key step to understanding how to preserve, manage and possibly optimize these complex ecosystems, especially in a changing climate. Using a random mutagenesis approach in a natural A. thaliana ecotype, we find that constitutively upregulated defenses are associated with both tolerance to (a)biotic threats and healthy recruitment of leaf bacteria, very likely in a direct manner. Thus, immunity and bacterial recruitment in leaves operate in parallel. Synthetic community experiments show further that this link plays important roles in shaping plant resilience to heat stress, an important consideration in developing plants more stable to climate change.
Significance Statement Plants are living ecosystems colonized by diverse microorganisms who strongly shape host health. Understanding how balance arises in host-associated microbiomes is a key step to understanding how to preserve, manage and possibly optimize these complex ecosystems, especially in a changing climate. Using a random mutagenesis approach in a natural A. thaliana ecotype, we find that constitutively upregulated defenses are associated with both tolerance to (a)biotic threats and healthy recruitment of leaf bacteria, very likely in a direct manner. Thus, immunity and bacterial recruitment in leaves operate in parallel. Synthetic community experiments show further that this link plays important roles in shaping plant resilience to heat stress, an important consideration in developing plants more stable to climate change.
2023
Klassert, Tilman E.; Hölzer, Martin; Zubiria-Barrera, Cristina; Bethge, Julia; Klaile, Esther; Müller, Mario M.; Marz, Manja; Slevogt, Hortense
Differential Transcriptional Responses of Human Granulocytes to Fungal Infection with Candida albicans and Aspergillus fumigatus Journal Article
In: J Fungi, vol. 9, iss. 10, pp. 1014, 2023.
Abstract | Links | BibTeX | Tags: differential expression analysis, fungi, RNA / transcriptomics
@article{nokey,
title = {Differential Transcriptional Responses of Human Granulocytes to Fungal Infection with \textit{Candida albicans} and \textit{Aspergillus fumigatus}},
author = {Tilman E. Klassert and Martin Hölzer and Cristina Zubiria-Barrera and Julia Bethge and Esther Klaile and Mario M. Müller and Manja Marz and Hortense Slevogt},
doi = {doi.org/10.3390/jof9101014},
year = {2023},
date = {2023-10-14},
journal = {J Fungi},
volume = {9},
issue = {10},
pages = {1014},
abstract = {Neutrophils are critical phagocytic cells in innate immunity, playing a significant role in defending against invasive fungal pathogens. This study aimed to explore the transcriptional activation of human neutrophils in response to different fungal pathogens, including Candida albicans and Aspergillus fumigatus, compared to the bacterial pathogen Escherichia coli. We identified distinct transcriptional profiles and stress-related pathways in neutrophils during fungal infections, highlighting their functional diversity and adaptability. The transcriptional response was largely redundant across all pathogens in immune-relevant categories and cytokine pathway activation. However, differences in the magnitude of differentially expressed genes (DEGs) were observed, with A. fumigatus inducing a lower transcriptional effect compared to C. albicans and E. coli. Notably, specific gene signatures associated with cell death were differentially regulated by fungal pathogens, potentially increasing neutrophil susceptibility to autophagy, pyroptosis, and neutrophil extracellular trap (NET) formation. These findings provide valuable insights into the complex immunological responses of neutrophils during fungal infections, offering new avenues for diagnostic and therapeutic strategies, particularly in the management of invasive fungal diseases.},
keywords = {differential expression analysis, fungi, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
Neutrophils are critical phagocytic cells in innate immunity, playing a significant role in defending against invasive fungal pathogens. This study aimed to explore the transcriptional activation of human neutrophils in response to different fungal pathogens, including Candida albicans and Aspergillus fumigatus, compared to the bacterial pathogen Escherichia coli. We identified distinct transcriptional profiles and stress-related pathways in neutrophils during fungal infections, highlighting their functional diversity and adaptability. The transcriptional response was largely redundant across all pathogens in immune-relevant categories and cytokine pathway activation. However, differences in the magnitude of differentially expressed genes (DEGs) were observed, with A. fumigatus inducing a lower transcriptional effect compared to C. albicans and E. coli. Notably, specific gene signatures associated with cell death were differentially regulated by fungal pathogens, potentially increasing neutrophil susceptibility to autophagy, pyroptosis, and neutrophil extracellular trap (NET) formation. These findings provide valuable insights into the complex immunological responses of neutrophils during fungal infections, offering new avenues for diagnostic and therapeutic strategies, particularly in the management of invasive fungal diseases.
Micheel, Julia; Aron, Franziska; Kelani, Abdulrahman A.; Girbardt, Christian; Blango, Matthew G.; Walther, Grit; Wollny, Damian
RNA-based sensitive fungal pathogen detection Journal Article
In: bioRxiv, 2023.
Abstract | Links | BibTeX | Tags: fungi, ncRNAs, RNA / transcriptomics
@article{nokey_46,
title = {RNA-based sensitive fungal pathogen detection},
author = {Julia Micheel and Franziska Aron and Abdulrahman A. Kelani and Christian Girbardt and Matthew G. Blango and Grit Walther and Damian Wollny},
doi = {10.1101/2023.09.26.559494},
year = {2023},
date = {2023-09-26},
urldate = {2023-09-26},
journal = {bioRxiv},
abstract = {Detecting fungal pathogens, a major cause of severe systemic infections, remains challenging due to the difficulty and time-consuming nature of diagnostic methods. This delay in identification hinders targeted treatment decisions and may lead to unnecessary use of broad-spectrum antibiotics. To expedite treatment initiation, one promising approach is to directly detect pathogen nucleic acids such as DNA, which is often preferred to RNA because of its inherent stability. However, a higher number of RNA molecules per cell makes RNA a more promising diagnostic target which is particularly prominent for highly expressed genes such as rRNA. Here, we investigated the utility of a minimal input-specialized reverse transcription protocol to increase diagnostic sensitivity. This proof-of-concept study demonstrates that fungal rRNA detection by the minimal input protocol is drastically more sensitive compared to detection of genomic DNA even with high levels of human RNA background. This approach can detect several of the most relevant human pathogenic fungal genera, such as Aspergillus, Candida, and Fusarium and thus represents a powerful, cheap, and easily adaptable addition to currently available diagnostic assays.},
keywords = {fungi, ncRNAs, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
Detecting fungal pathogens, a major cause of severe systemic infections, remains challenging due to the difficulty and time-consuming nature of diagnostic methods. This delay in identification hinders targeted treatment decisions and may lead to unnecessary use of broad-spectrum antibiotics. To expedite treatment initiation, one promising approach is to directly detect pathogen nucleic acids such as DNA, which is often preferred to RNA because of its inherent stability. However, a higher number of RNA molecules per cell makes RNA a more promising diagnostic target which is particularly prominent for highly expressed genes such as rRNA. Here, we investigated the utility of a minimal input-specialized reverse transcription protocol to increase diagnostic sensitivity. This proof-of-concept study demonstrates that fungal rRNA detection by the minimal input protocol is drastically more sensitive compared to detection of genomic DNA even with high levels of human RNA background. This approach can detect several of the most relevant human pathogenic fungal genera, such as Aspergillus, Candida, and Fusarium and thus represents a powerful, cheap, and easily adaptable addition to currently available diagnostic assays.
Förstner, Konrad U.; Becker, Anke; Blom, Jochen; Bork, Peer; Clavel, Thomas; Dieckmann, Marius; Goesmann, Alexander; Götz, Barbara; Gübitz, Thomas; Hufsky, Franziska; Jünemann, Sebastian; Körner, Marie-Louise; Marz, Manja; Rocha, Ulisses Nunes Da; Overmann, Jörg; Pühler, Alfred; Rebholz-Schuhmann, Dietrich; Sczyrba, Alexander; Stoye, Jens; Vandendorpe, Justine; Rossum, Thea Van; McHardy, Alice
NFDI4Microbiota – national research data infrastructure for microbiota research Journal Article
In: Research Ideas and Outcomes, vol. 9, pp. e110501, 2023.
Abstract | Links | BibTeX | Tags: bacteria, fungi, viruses
@article{nokey,
title = {NFDI4Microbiota – national research data infrastructure for microbiota research},
author = {Konrad U. Förstner and Anke Becker and Jochen Blom and Peer Bork and Thomas Clavel and Marius Dieckmann and Alexander Goesmann and Barbara Götz and Thomas Gübitz and Franziska Hufsky and Sebastian Jünemann and Marie-Louise Körner and Manja Marz and Ulisses Nunes Da Rocha and Jörg Overmann and Alfred Pühler and Dietrich Rebholz-Schuhmann and Alexander Sczyrba and Jens Stoye and Justine Vandendorpe and Thea Van Rossum and Alice McHardy},
doi = {10.3897/rio.9.e110501},
year = {2023},
date = {2023-08-24},
journal = {Research Ideas and Outcomes},
volume = {9},
pages = {e110501},
abstract = {Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany.},
keywords = {bacteria, fungi, viruses},
pubstate = {published},
tppubtype = {article}
}
Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany.
2021
Martín-Hernández, Giselle C; Müller, Bettina; Chmielarz, Mikołaj; Brandt, Christian; Hölzer, Martin; Viehweger, Adrian; Passoth, Volkmar
Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14 Journal Article
In: Genomics, vol. 113, no. 6, pp. 4022-4027, 2021.
Abstract | Links | BibTeX | Tags: annotation, assembly, DNA / genomics, fungi, nanopore
@article{Martín-Hernández2021,
title = {Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14},
author = {Giselle C Martín-Hernández and Bettina Müller and Mikołaj Chmielarz and Christian Brandt and Martin Hölzer and Adrian Viehweger and Volkmar Passoth
},
doi = {10.1016/j.ygeno.2021.10.006},
year = {2021},
date = {2021-10-11},
urldate = {2021-10-11},
journal = {Genomics},
volume = {113},
number = {6},
pages = {4022-4027},
abstract = {Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size of the genome is 20,534,857 bp and the overall GC content is 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. We annotated 9464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes.},
keywords = {annotation, assembly, DNA / genomics, fungi, nanopore},
pubstate = {published},
tppubtype = {article}
}
Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size of the genome is 20,534,857 bp and the overall GC content is 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. We annotated 9464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes.
2019
Riege, Konstantin
2019.
Links | BibTeX | Tags: annotation, bacteria, fungi, ncRNAs, RNA / transcriptomics
@phdthesis{nokey,
title = {Annotation of non-coding RNAs and examination of Next Generation Sequencing data of pathogenic organisms},
author = {Konstantin Riege},
url = {https://suche.thulb.uni-jena.de/Record/1067866388},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
howpublished = {Friedrich-Schiller-Universität Jena},
keywords = {annotation, bacteria, fungi, ncRNAs, RNA / transcriptomics},
pubstate = {published},
tppubtype = {phdthesis}
}
2017
Riege, Konstantin; Hölzer, Martin; Klassert, Tilman E; Barth, Emanuel; Bräuer, Julia; Collatz, Maximilian; Hufsky, Franziska; Mostajo, Nelly F.; Stock, Magdalena; Vogel, Bertram; Slevogt, Hortense; Marz, Manja
Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D Journal Article
In: Sci Rep, vol. 7, pp. 40598, 2017.
Abstract | Links | BibTeX | Tags: bacteria, differential expression analysis, fungi, ncRNAs, RNA / transcriptomics
@article{Riege:17,
title = {Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D},
author = {Konstantin Riege and Martin Hölzer and Tilman E Klassert and Emanuel Barth and Julia Bräuer and Maximilian Collatz and Franziska Hufsky and Nelly F. Mostajo and Magdalena Stock and Bertram Vogel and Hortense Slevogt and Manja Marz},
doi = {10.1038/srep40598},
year = {2017},
date = {2017-01-17},
urldate = {2017-01-17},
journal = {Sci Rep},
volume = {7},
pages = {40598},
abstract = {Mycoses induced by C.albicans or A.fumigatus can cause important host damage either by deficient or exaggerated immune response. Regulation of chemokine and cytokine signaling plays a crucial role for an adequate inflammation, which can be modulated by vitamins A and D. Non-coding RNAs (ncRNAs) as transcription factors or cis-acting antisense RNAs are known to be involved in gene regulation. However, the processes during fungal infections and treatment with vitamins in terms of therapeutic impact are unknown. We show that in monocytes both vitamins regulate ncRNAs involved in amino acid metabolism and immune system processes using comprehensive RNA-Seq analyses. Compared to protein-coding genes, fungi and bacteria induced an expression change in relatively few ncRNAs, but with massive fold changes of up to 4000. We defined the landscape of long-ncRNAs (lncRNAs) in response to pathogens and observed variation in the isoforms composition for several lncRNA following infection and vitamin treatment. Most of the involved antisense RNAs are regulated and positively correlated with their sense protein-coding genes. We investigated lncRNAs with stimulus specific immunomodulatory activity as potential marker genes: LINC00595, SBF2-AS1 (A.fumigatus) and RP11-588G21.2, RP11-394l13.1 (C.albicans) might be detectable in the early phase of infection and serve as therapeutic targets in the future.},
keywords = {bacteria, differential expression analysis, fungi, ncRNAs, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
Mycoses induced by C.albicans or A.fumigatus can cause important host damage either by deficient or exaggerated immune response. Regulation of chemokine and cytokine signaling plays a crucial role for an adequate inflammation, which can be modulated by vitamins A and D. Non-coding RNAs (ncRNAs) as transcription factors or cis-acting antisense RNAs are known to be involved in gene regulation. However, the processes during fungal infections and treatment with vitamins in terms of therapeutic impact are unknown. We show that in monocytes both vitamins regulate ncRNAs involved in amino acid metabolism and immune system processes using comprehensive RNA-Seq analyses. Compared to protein-coding genes, fungi and bacteria induced an expression change in relatively few ncRNAs, but with massive fold changes of up to 4000. We defined the landscape of long-ncRNAs (lncRNAs) in response to pathogens and observed variation in the isoforms composition for several lncRNA following infection and vitamin treatment. Most of the involved antisense RNAs are regulated and positively correlated with their sense protein-coding genes. We investigated lncRNAs with stimulus specific immunomodulatory activity as potential marker genes: LINC00595, SBF2-AS1 (A.fumigatus) and RP11-588G21.2, RP11-394l13.1 (C.albicans) might be detectable in the early phase of infection and serve as therapeutic targets in the future.
Klassert, Tilman E; Bräuer, Julia; Hölzer, Martin; Stock, Magdalena; Riege, Konstantin; Zubiría-Barrera, Cristina; Müller, Mario M; Rummler, Silke; Skerka, Christine; Marz, Manja; Slevogt, Hortense
Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection Journal Article
In: Sci Rep, vol. 7, pp. 40599, 2017.
Abstract | Links | BibTeX | Tags: bacteria, differential expression analysis, fungi, RNA / transcriptomics
@article{Klassert:17,
title = {Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection},
author = {Tilman E Klassert and Julia Bräuer and Martin Hölzer and Magdalena Stock and Konstantin Riege and Cristina Zubiría-Barrera and Mario M Müller and Silke Rummler and Christine Skerka and Manja Marz and Hortense Slevogt},
doi = {10.1038/srep40599},
year = {2017},
date = {2017-01-17},
urldate = {2017-01-17},
journal = {Sci Rep},
volume = {7},
pages = {40599},
abstract = {Vitamin A and vitamin D are essential nutrients with a wide range of pleiotropic effects in humans. Beyond their well-documented roles in cellular differentiation, embryogenesis, tissue maintenance and bone/calcium homeostasis, both vitamins have attracted considerable attention due to their association with-immunological traits. Nevertheless, our knowledge of their immunomodulatory potential during infection is restricted to single gene-centric studies, which do not reflect the complexity of immune processes. In the present study, we performed a comprehensive RNA-seq-based approach to define the whole immunomodulatory role of vitamins A and D during infection. Using human monocytes as host cells, we characterized the differential role of both vitamins upon infection with three different pathogens: Aspergillus fumigatus, Candida albicans and Escherichia coli. Both vitamins showed an unexpected ability to counteract the pathogen-induced transcriptional responses. Upon infection, we identified 346 and 176 immune-relevant genes that were regulated by atRA and vitD, respectively. This immunomodulatory activity was dependent on the inflammatory stimulus, allowing us to distinguish regulatory patterns which were specific for each stimulatory setting. Moreover, we explored possible direct and indirect mechanisms of vitamin-mediated regulation of the immune response. Our findings highlight the importance of vitamin-monitoring in critically ill patients. Moreover, our results underpin the potential of atRA and vitD as therapeutic options for anti-inflammatory treatment.},
keywords = {bacteria, differential expression analysis, fungi, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
Vitamin A and vitamin D are essential nutrients with a wide range of pleiotropic effects in humans. Beyond their well-documented roles in cellular differentiation, embryogenesis, tissue maintenance and bone/calcium homeostasis, both vitamins have attracted considerable attention due to their association with-immunological traits. Nevertheless, our knowledge of their immunomodulatory potential during infection is restricted to single gene-centric studies, which do not reflect the complexity of immune processes. In the present study, we performed a comprehensive RNA-seq-based approach to define the whole immunomodulatory role of vitamins A and D during infection. Using human monocytes as host cells, we characterized the differential role of both vitamins upon infection with three different pathogens: Aspergillus fumigatus, Candida albicans and Escherichia coli. Both vitamins showed an unexpected ability to counteract the pathogen-induced transcriptional responses. Upon infection, we identified 346 and 176 immune-relevant genes that were regulated by atRA and vitD, respectively. This immunomodulatory activity was dependent on the inflammatory stimulus, allowing us to distinguish regulatory patterns which were specific for each stimulatory setting. Moreover, we explored possible direct and indirect mechanisms of vitamin-mediated regulation of the immune response. Our findings highlight the importance of vitamin-monitoring in critically ill patients. Moreover, our results underpin the potential of atRA and vitD as therapeutic options for anti-inflammatory treatment.
2016
Barth, Emanuel; Hübler, Ron; Baniahmad, Aria; Marz, Manja
The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms Journal Article
In: Genome Biol Evol, vol. 8, no. 4, pp. 1279–1289, 2016.
Abstract | Links | BibTeX | Tags: bacteria, evolution, fungi, splicing
@article{Barth:16,
title = {The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms},
author = {Emanuel Barth and Ron Hübler and Aria Baniahmad and Manja Marz},
doi = {10.1093/gbe/evw073},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
journal = {Genome Biol Evol},
volume = {8},
number = {4},
pages = {1279--1289},
abstract = {The COP9 signalosome (CSN) is a highly conserved protein complex, recently being crystallized for human. In mammals and plants the COP9 complex consists of nine subunits, CSN 1-8 and CSNAP. The CSN regulates the activity of culling ring E3 ubiquitin and plays central roles in pleiotropy, cell cycle, and defense of pathogens. Despite the interesting and essential functions, a thorough analysis of the CSN subunits in evolutionary comparative perspective is missing. Here we compared 61 eukaryotic genomes including plants, animals, and yeasts genomes and show that the most conserved subunits of eukaryotes among the nine subunits are CSN2 and CSN5. This may indicate a strong evolutionary selection for these two subunits. Despite the strong conservation of the protein sequence, the genomic structures of the intron/exon boundaries indicate no conservation at genomic level. This suggests that the gene structure is exposed to a much less selection compared with the protein sequence. We also show the conservation of important active domains, such as PCI (proteasome lid-CSN-initiation factor) and MPN (MPR1/PAD1 amino-terminal). We identified novel exons and alternative splicing variants for all CSN subunits. This indicates another level of complexity of the CSN. Notably, most COP9-subunits were identified in all multicellular and unicellular eukaryotic organisms analyzed, but not in prokaryotes or archaeas. Thus, genes encoding CSN subunits present in all analyzed eukaryotes indicate the invention of the signalosome at the root of eukaryotes. The identification of alternative splice variants indicates possible "mini-complexes" or COP9 complexes with independent subunits containing potentially novel and not yet identified functions.},
keywords = {bacteria, evolution, fungi, splicing},
pubstate = {published},
tppubtype = {article}
}
The COP9 signalosome (CSN) is a highly conserved protein complex, recently being crystallized for human. In mammals and plants the COP9 complex consists of nine subunits, CSN 1-8 and CSNAP. The CSN regulates the activity of culling ring E3 ubiquitin and plays central roles in pleiotropy, cell cycle, and defense of pathogens. Despite the interesting and essential functions, a thorough analysis of the CSN subunits in evolutionary comparative perspective is missing. Here we compared 61 eukaryotic genomes including plants, animals, and yeasts genomes and show that the most conserved subunits of eukaryotes among the nine subunits are CSN2 and CSN5. This may indicate a strong evolutionary selection for these two subunits. Despite the strong conservation of the protein sequence, the genomic structures of the intron/exon boundaries indicate no conservation at genomic level. This suggests that the gene structure is exposed to a much less selection compared with the protein sequence. We also show the conservation of important active domains, such as PCI (proteasome lid-CSN-initiation factor) and MPN (MPR1/PAD1 amino-terminal). We identified novel exons and alternative splicing variants for all CSN subunits. This indicates another level of complexity of the CSN. Notably, most COP9-subunits were identified in all multicellular and unicellular eukaryotic organisms analyzed, but not in prokaryotes or archaeas. Thus, genes encoding CSN subunits present in all analyzed eukaryotes indicate the invention of the signalosome at the root of eukaryotes. The identification of alternative splice variants indicates possible "mini-complexes" or COP9 complexes with independent subunits containing potentially novel and not yet identified functions.
2015
Linde, Jörg; Duggan, Seána; Weber, Michael; Horn, Fabian; Sieber, Patricia; Hellwig, Daniela; Riege, Konstantin; Marz, Manja; Martin, Ronny; Guthke, Reinhard; Kurzai, Oliver
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq Journal Article
In: Nucleic Acids Res, vol. 43, no. 3, pp. 1392–1406, 2015.
Abstract | Links | BibTeX | Tags: annotation, fungi, RNA / transcriptomics, splicing
@article{Linde:15,
title = {Defining the transcriptomic landscape of \textit{Candida glabrata} by RNA-Seq},
author = {Jörg Linde and Seána Duggan and Michael Weber and Fabian Horn and Patricia Sieber and Daniela Hellwig and Konstantin Riege and Manja Marz and Ronny Martin and Reinhard Guthke and Oliver Kurzai},
doi = {10.1093/nar/gku1357},
year = {2015},
date = {2015-01-13},
urldate = {2015-01-13},
journal = {Nucleic Acids Res},
volume = {43},
number = {3},
pages = {1392--1406},
abstract = {Candida glabrata is the second most common pathogenic Candida species and has emerged as a leading cause of nosocomial fungal infections. Its reduced susceptibility to antifungal drugs and its close relationship to Saccharomyces cerevisiae make it an interesting research focus. Although its genome sequence was published in 2004, little is known about its transcriptional dynamics. Here, we provide a detailed RNA-Seq-based analysis of the transcriptomic landscape of C. glabrata in nutrient-rich media, as well as under nitrosative stress and during pH shift. Using RNA-Seq data together with state-of-the-art gene prediction tools, we refined the annotation of the C. glabrata genome and predicted 49 novel protein-coding genes. Of these novel genes, 14 have homologs in S. cerevisiae and six are shared with other Candida species. We experimentally validated four novel protein-coding genes of which two are differentially regulated during pH shift and interaction with human neutrophils, indicating a potential role in host-pathogen interaction. Furthermore, we identified 58 novel non-protein-coding genes, 38 new introns and condition-specific alternative splicing. Finally, our data suggest different patterns of adaptation to pH shift and nitrosative stress in C. glabrata, Candida albicans and S. cerevisiae and thus further underline a distinct evolution of virulence in yeast.},
keywords = {annotation, fungi, RNA / transcriptomics, splicing},
pubstate = {published},
tppubtype = {article}
}
Candida glabrata is the second most common pathogenic Candida species and has emerged as a leading cause of nosocomial fungal infections. Its reduced susceptibility to antifungal drugs and its close relationship to Saccharomyces cerevisiae make it an interesting research focus. Although its genome sequence was published in 2004, little is known about its transcriptional dynamics. Here, we provide a detailed RNA-Seq-based analysis of the transcriptomic landscape of C. glabrata in nutrient-rich media, as well as under nitrosative stress and during pH shift. Using RNA-Seq data together with state-of-the-art gene prediction tools, we refined the annotation of the C. glabrata genome and predicted 49 novel protein-coding genes. Of these novel genes, 14 have homologs in S. cerevisiae and six are shared with other Candida species. We experimentally validated four novel protein-coding genes of which two are differentially regulated during pH shift and interaction with human neutrophils, indicating a potential role in host-pathogen interaction. Furthermore, we identified 58 novel non-protein-coding genes, 38 new introns and condition-specific alternative splicing. Finally, our data suggest different patterns of adaptation to pH shift and nitrosative stress in C. glabrata, Candida albicans and S. cerevisiae and thus further underline a distinct evolution of virulence in yeast.
2014
Schwartze, Volker U.; Winter, Sascha; Shelest, Ekaterina; Marcet-Houben, Marina; Horn, Fabian; Wehner, Stefanie; Linde, Jörg; Valiante, Vito; Sammeth, Michael; Riege, Konstantin; Nowrousian, Minou; Kaerger, Kerstin; Jacobsen, Ilse D.; Marz, Manja; Brakhage, Axel A.; Gabaldón, Toni; Böcker, Sebastian; Voigt, Kerstin
In: PLos Genet, vol. 10, pp. e1004496, 2014.
Abstract | Links | BibTeX | Tags: ancient DNA, assembly, evolution, fungi, RNA / transcriptomics, splicing
@article{Schwartze:14,
title = {Gene expansion shapes genome architecture in the human pathogen \textit{Lichtheimia corymbifera}: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)},
author = {Volker U. Schwartze and Sascha Winter and Ekaterina Shelest and Marina Marcet-Houben and Fabian Horn and Stefanie Wehner and Jörg Linde and Vito Valiante and Michael Sammeth and Konstantin Riege and Minou Nowrousian and Kerstin Kaerger and Ilse D. Jacobsen and Manja Marz and Axel A. Brakhage and Toni Gabaldón and Sebastian Böcker and Kerstin Voigt},
doi = {10.1371/journal.pgen.1004496},
year = {2014},
date = {2014-08-14},
urldate = {2014-08-14},
journal = {PLos Genet},
volume = {10},
pages = {e1004496},
abstract = {Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.},
keywords = {ancient DNA, assembly, evolution, fungi, RNA / transcriptomics, splicing},
pubstate = {published},
tppubtype = {article}
}
Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.
2012
Qi, Xiaodong; Li, Yang; Honda, Shinji; Hoffmann, Steve; Marz, Manja; Mosig, Axel; Podlevsky, Joshua D; Stadler, Peter F; Selker, Eric U; Chen, Julian J-L
The common ancestral core of vertebrate and fungal telomerase RNAs Journal Article
In: Nucleic Acids Res, vol. 41, pp. 450–462, 2012.
Abstract | Links | BibTeX | Tags: evolution, fungi, phylogenetics
@article{Qi:13,
title = {The common ancestral core of vertebrate and fungal telomerase RNAs},
author = {Xiaodong Qi and Yang Li and Shinji Honda and Steve Hoffmann and Manja Marz and Axel Mosig and Joshua D Podlevsky and Peter F Stadler and Eric U Selker and Julian J-L Chen},
doi = {10.1093/nar/gks980},
year = {2012},
date = {2012-10-23},
urldate = {2012-10-23},
journal = {Nucleic Acids Res},
volume = {41},
pages = {450--462},
abstract = {Telomerase is a ribonucleoprotein with an intrinsic telomerase RNA (TER) component. Within yeasts, TER is remarkably large and presents little similarity in secondary structure to vertebrate or ciliate TERs. To better understand the evolution of fungal telomerase, we identified 74 TERs from Pezizomycotina and Taphrinomycotina subphyla, sister clades to budding yeasts. We initially identified TER from Neurospora crassa using a novel deep-sequencing-based approach, and homologous TER sequences from available fungal genome databases by computational searches. Remarkably, TERs from these non-yeast fungi have many attributes in common with vertebrate TERs. Comparative phylogenetic analysis of highly conserved regions within Pezizomycotina TERs revealed two core domains nearly identical in secondary structure to the pseudoknot and CR4/5 within vertebrate TERs. We then analyzed N. crassa and Schizosaccharomyces pombe telomerase reconstituted in vitro, and showed that the two RNA core domains in both systems can reconstitute activity in trans as two separate RNA fragments. Furthermore, the primer-extension pulse-chase analysis affirmed that the reconstituted N. crassa telomerase synthesizes TTAGGG repeats with high processivity, a common attribute of vertebrate telomerase. Overall, this study reveals the common ancestral cores of vertebrate and fungal TERs, and provides insights into the molecular evolution of fungal TER structure and function.},
keywords = {evolution, fungi, phylogenetics},
pubstate = {published},
tppubtype = {article}
}
Telomerase is a ribonucleoprotein with an intrinsic telomerase RNA (TER) component. Within yeasts, TER is remarkably large and presents little similarity in secondary structure to vertebrate or ciliate TERs. To better understand the evolution of fungal telomerase, we identified 74 TERs from Pezizomycotina and Taphrinomycotina subphyla, sister clades to budding yeasts. We initially identified TER from Neurospora crassa using a novel deep-sequencing-based approach, and homologous TER sequences from available fungal genome databases by computational searches. Remarkably, TERs from these non-yeast fungi have many attributes in common with vertebrate TERs. Comparative phylogenetic analysis of highly conserved regions within Pezizomycotina TERs revealed two core domains nearly identical in secondary structure to the pseudoknot and CR4/5 within vertebrate TERs. We then analyzed N. crassa and Schizosaccharomyces pombe telomerase reconstituted in vitro, and showed that the two RNA core domains in both systems can reconstitute activity in trans as two separate RNA fragments. Furthermore, the primer-extension pulse-chase analysis affirmed that the reconstituted N. crassa telomerase synthesizes TTAGGG repeats with high processivity, a common attribute of vertebrate telomerase. Overall, this study reveals the common ancestral cores of vertebrate and fungal TERs, and provides insights into the molecular evolution of fungal TER structure and function.
2010
Yusuf, Dilmurat; Marz, Manja; Stadler, Peter F; Hofacker, Ivo L
Bcheck: a wrapper tool for detecting RNase P RNA genes Journal Article
In: BMC Genomics, vol. 11, pp. 432, 2010.
Abstract | Links | BibTeX | Tags: annotation, bacteria, classification, fungi, ncRNAs, RNA / transcriptomics, software
@article{Yusuf:10,
title = {Bcheck: a wrapper tool for detecting RNase P RNA genes},
author = {Dilmurat Yusuf and Manja Marz and Peter F Stadler and Ivo L Hofacker},
url = {http://rna.tbi.univie.ac.at/bcheck},
doi = {10.1186/1471-2164-11-432},
year = {2010},
date = {2010-07-13},
urldate = {2010-07-13},
journal = {BMC Genomics},
volume = {11},
pages = {432},
abstract = {Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily specific descriptor models and covariance models. Scanning all microbial genomes in GenBank identifies RNase P RNA genes in 98% of 1024 microbial chromosomal sequences within just 4 hours on single CPU. Comparing to existing annotations found in 387 of the GenBank files, Bcheck predictions have more intact structure and are automatically classified by subfamily membership. For eukaryotic chromosomes Bcheck could identify the known RNase P RNA genes in 84 out of 85 metazoan genomes and 19 out of 21 fungi genomes. Bcheck predicted 37 novel eukaryotic RNase P RNA genes, 32 of which are from fungi. Gene duplication events are observed in at least 20 metazoan organisms. Scanning of meta-genomic data from the Global Ocean Sampling Expedition, comprising over 10 million sample sequences (18 Gigabases), predicted 2909 unique genes, 98% of which fall into ancestral bacteria A type of RNase P RNA and 66% of which have no close homolog to known prokaryotic RNase P RNA. The combination of efficient filtering by means of a descriptor-based search and subsequent construction of a high-quality gene model by means of a covariance model provides an efficient method for the detection of RNase P RNA genes in large-scale sequencing data. Bcheck is implemented as webserver and can also be downloaded for local use from http://rna.tbi.univie.ac.at/bcheck.},
keywords = {annotation, bacteria, classification, fungi, ncRNAs, RNA / transcriptomics, software},
pubstate = {published},
tppubtype = {article}
}
Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily specific descriptor models and covariance models. Scanning all microbial genomes in GenBank identifies RNase P RNA genes in 98% of 1024 microbial chromosomal sequences within just 4 hours on single CPU. Comparing to existing annotations found in 387 of the GenBank files, Bcheck predictions have more intact structure and are automatically classified by subfamily membership. For eukaryotic chromosomes Bcheck could identify the known RNase P RNA genes in 84 out of 85 metazoan genomes and 19 out of 21 fungi genomes. Bcheck predicted 37 novel eukaryotic RNase P RNA genes, 32 of which are from fungi. Gene duplication events are observed in at least 20 metazoan organisms. Scanning of meta-genomic data from the Global Ocean Sampling Expedition, comprising over 10 million sample sequences (18 Gigabases), predicted 2909 unique genes, 98% of which fall into ancestral bacteria A type of RNase P RNA and 66% of which have no close homolog to known prokaryotic RNase P RNA. The combination of efficient filtering by means of a descriptor-based search and subsequent construction of a high-quality gene model by means of a covariance model provides an efficient method for the detection of RNase P RNA genes in large-scale sequencing data. Bcheck is implemented as webserver and can also be downloaded for local use from http://rna.tbi.univie.ac.at/bcheck.