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7. The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus

Author

Furukawa, Takanori, van Rhijn, Norman, Fraczek, Marcin, Gsaller, Fabio, Davies, Emma, Carr, Paul, Gago, Sara, Fortune-Grant, Rachael, Rahman, Sayema, Gilsenan, Jane Mabey, Houlder, Emma, Kowalski, Caitlin H., Raj, Shriya, Paul, Sanjoy, Cook, Peter, Parker, Josie E., Kelly, Steve, Cramer, Robert A., Latgé, Jean-Paul, Moye-Rowley, Scott, Bignell, Elaine, Bowyer, Paul, and Bromley, Michael J.

Published
2020
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26. Large-scale profiling of noncoding RNA function in yeast

Author

Parker, Steven, Fraczek, Marcin G., Wu, Jian, Shamsah, Sara, Manousaki, Alkisti, Dungrattanalert, Kobchai, de Almeida, Rogerio Alves, Invernizzi, Edith, Burgis, Tim, Omara, Walid, Griffiths-Jones, Sam, Delneri, Daniela, and O’Keefe, Raymond T.

Subjects
deletion collection, Heterozygote, RNA, Untranslated, 3' Utr, lcsh:QH426-470, Yeast and Fungal Models, Saccharomyces cerevisiae, Haploidy, Research and Analysis Methods, Biochemistry, Noncoding RNA, Saccharomyces, Model Organisms, Untranslated Regions, Gene Expression Regulation, Fungal, Manchester Institute of Biotechnology, Databases, Genetic, Fitness, Genetics, Small nucleolar RNAs, Non-coding RNA, Evolutionary Biology, Biology and life sciences, Population Biology, Messenger RNA, Gene Expression Profiling, Organisms, Fungi, Eukaryota, RNA, Fungal, Functional genomics, Gene Pool, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, Yeast, Gene regulation, Nucleic acids, lcsh:Genetics, Phenotype, Experimental Organism Systems, RNA, Gene expression, Genetic Fitness, Transfer RNA, Population Genetics, Gene Deletion, Research Article
Abstract

Noncoding RNAs (ncRNAs) are emerging as key regulators of cellular function. We have exploited the recently developed barcoded ncRNA gene deletion strain collections in the yeast Saccharomyces cerevisiae to investigate the numerous ncRNAs in yeast with no known function. The ncRNA deletion collection contains deletions of tRNAs, snoRNAs, snRNAs, stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs) and other annotated ncRNAs encompassing 532 different individual ncRNA deletions. We have profiled the fitness of the diploid heterozygous ncRNA deletion strain collection in six conditions using batch and continuous liquid culture, as well as the haploid ncRNA deletion strain collections arrayed individually onto solid rich media. These analyses revealed many novel environmental-specific haplo-insufficient and haplo-proficient phenotypes providing key information on the importance of each specific ncRNA in every condition. Co-fitness analysis using fitness data from the heterozygous ncRNA deletion strain collection identified two ncRNA groups required for growth during heat stress and nutrient deprivation. The extensive fitness data for each ncRNA deletion strain has been compiled into an easy to navigate database called Yeast ncRNA Analysis (YNCA). By expanding the original ncRNA deletion strain collection we identified four novel essential ncRNAs; SUT527, SUT075, SUT367 and SUT259/691. We defined the effects of each new essential ncRNA on adjacent gene expression in the heterozygote background identifying both repression and induction of nearby genes. Additionally, we discovered a function for SUT527 in the expression, 3’ end formation and localization of SEC4, an essential protein coding mRNA. Finally, using plasmid complementation we rescued the SUT075 lethal phenotype revealing that this ncRNA acts in trans. Overall, our findings provide important new insights into the function of ncRNAs., Author summary Genomes from different organisms produce noncoding RNAs that are not translated to make proteins and whose functions are largely unknown. There are approximately 2,000 noncoding RNAs that make up almost 25% of the yeast genome compared to the approximately 6,000 protein coding genes that make up 70% of the yeast genome. With this large number of ncRNAs there is a need for large-scale studies to determine the functional roles of ncRNAs. We take advantage of a recently developed resource of 532 yeast strains in which individual noncoding RNA genes have been deleted. We grow these yeast noncoding RNA deletion strains in different conditions and catalogue how each noncoding RNA contributes to cell growth. Improvement or inhibition of cell growth under particular conditions implicates the deleted RNA in cellular responses to those conditions. We have also investigated in more detail the function of specific noncoding RNAs, revealing examples of how a deletion influences nearby genes, and other examples of noncoding RNAs that regulate genes at distant genomic locations. We have made our extensive data on the fitness of noncoding RNA deletion mutants publically available for searching and bulk download in a new online resource, called Yeast ncRNA Analysis (YNCA). This large-scale analysis of noncoding RNA deletion mutants reveals the importance of many noncoding RNAs in cellular function.

Published
2018

28. High‐Throughput Gene Replacement in Aspergillus fumigatus

Author

Zhao, Can, primary, Fraczek, Marcin G., additional, Dineen, Lauren, additional, Lebedinec, Ressa, additional, Macheleidt, Juliane, additional, Heinekamp, Thorsten, additional, Delneri, Daniela, additional, Bowyer, Paul, additional, Brakhage, Axel A., additional, and Bromley, Michael, additional

Published
2019
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29. Aspergillus fumigatus allergen expression is coordinately regulated in response to hydrogen peroxide and cyclic AMP

Author

Bowyer Paul, Denning David W, Denson Marian, Rashid Rifat, and Fraczek Marcin G

Subjects
Immunologic diseases. Allergy, RC581-607
Abstract

Abstract Background A. fumigatus has been associated with a wide spectrum of allergic disorders such as ABPA or SAFS. It is poorly understood what allergens in particular are being expressed during fungal invasion and which are responsible for stimulation of immune responses. Study of the dynamics of allergen production by fungi may lead to insights into how allergens are presented to the immune system. Methods Expression of 17 A. fumigatus allergen genes was examined in response to various culture conditions and stimuli as well as in the presence of macrophages in order to mimic conditions encountered in the lung. Results Expression of 14/17 allergen genes was strongly induced by oxidative stress caused by hydrogen peroxide (Asp f 1, -2, -4, -5, -6, -7, -8, -10, -13, -17 and -18, all >10-fold and Asp f 11, -12, and -22, 5-10-fold) and 16/17 allergen genes were repressed in the presence of cAMP. The 4 protease allergen genes (Asp f -5, -10, -13 and -18) were expressed at very low levels compared to the comparator (β-tubulin) under all other conditions examined. Mild heat shock, anoxia, lipid and presence of macrophages did not result in coordinated changes in allergen gene expression. Growth on lipid as sole carbon source contributed to the moderate induction of most of the allergen genes. Heat shock (37°C > 42°C) caused moderate repression in 11/17 genes (Asp f 1, -2, -4, -5, -6, -9, -10, -13, -17, -18 and -23) (2- to 9-fold), which was mostly evident for Asp f 1 and -9 (~9-fold). Anaerobic stress led to moderate induction of 13/17 genes (1.1 to 4-fold) with one, Asp f 8 induced over 10-fold when grown under mineral oil. Complex changes were seen in gene expression during co-culture of A. fumigatus with macrophages. Conclusions Remarkable coordination of allergen gene expression in response to a specific condition (oxidative stress or the presence of cAMP) has been observed, implying that a single biological stimulus may play a role in allergen gene regulation. Interdiction of a putative allergen expression induction signalling pathway might provide a novel therapy for treatment of fungal allergy.

Published
2010
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30. Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues

Author

Fraczek Marcin, Bowyer Paul, and Denning David W

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Allergy is a common debilitating and occasionally life threatening condition. The fungal kingdom contains a number of species that produce a wide range of well defined protein allergens although the vast majority of fungal species have unknown allergenic potential. The recent genome sequencing of a variety of fungi provides the opportunity to assess the occurrence of allergen orthologues across the fungal kingdom. Here we use comparative genomics to survey the occurrence of allergen orthologues in fungi. Results A database of 82 allergen sequences was compiled and used to search 22 fungal genomes. Additionally we were able to model allergen structure for representative members of several highly homologous allergen orthologue classes. We found that some allergen orthologue classes that had predicted structural congruence to allergens and allergen epitopes were ubiquitous in all fungi. Other allergen orthologues classes were less well conserved and may not possess conserved allergen epitope orthologues in all fungi. A final group of allergen orthologues, including the major allergens Asp f 1 and Alt a 1, appear to be present in only a limited number of species. Conclusion These results imply that most fungi may possess proteins that have potential to be allergens or to cross react with allergens. This, together with the observation that important allergens such as Asp f 1 are limited to genera or species, has significant implications for understating fungal sensitization, and interpreting diagnosis and management of fungal allergy.

Published
2006
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31. A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae

Author

Parker, Steven, Fraczek, Marcin G., Wu, Jian, Shamsah, Sara, Manousaki, Alkisti, Dungrattanalert, Kobchai, de Almeida, Rogerio Alves, Estrada-Rivadeneyra, Diego, Omara, Walid, Delneri, Daniela, and O'Keefe, Raymond T.

Subjects
RNA, Untranslated, snRNA, Report, RNA, Fungal, Saccharomyces cerevisiae, yeast, Genome, Fungal, snoRNA, ncRNA, tRNA, Sequence Deletion
Abstract

Eukaryotic genomes are extensively transcribed, generating many different RNAs with no known function. We have constructed 1502 molecular barcoded ncRNA gene deletion strains encompassing 443 ncRNAs in the yeast Saccharomyces cerevisiae as tools for ncRNA functional analysis. This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown. Specifically, deletions have been constructed for ncRNAs found in the intergenic regions, not overlapping genes or their promoters (i.e., at least 200 bp minimum distance from the closest gene start codon). The deletion strains carry molecular barcodes designed to be complementary with the protein gene deletion collection enabling parallel analysis experiments. These strains will be useful for the numerous genomic and molecular techniques that utilize deletion strains, including genome-wide phenotypic screens under different growth conditions, pooled chemogenomic screens with drugs or chemicals, synthetic genetic array analysis to uncover novel genetic interactions, and synthetic dosage lethality screens to analyze gene dosage. Overall, we created a valuable resource for the RNA community and for future ncRNA research.

Published
2017

33. Large-scale profiling of noncoding RNA function in yeast

Author

Parker, Steven, primary, Fraczek, Marcin G., additional, Wu, Jian, additional, Shamsah, Sara, additional, Manousaki, Alkisti, additional, Dungrattanalert, Kobchai, additional, de Almeida, Rogerio Alves, additional, Invernizzi, Edith, additional, Burgis, Tim, additional, Omara, Walid, additional, Griffiths-Jones, Sam, additional, Delneri, Daniela, additional, and O’Keefe, Raymond T., additional

Published
2018
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35. Correction: Mitochondrial Complex I Is a Global Regulator of Secondary Metabolism, Virulence and Azole Sensitivity in Fungi

Author

Bromley, Mike, primary, Johns, Anna, additional, Davies, Emma, additional, Fraczek, Marcin, additional, Gilsenan, Jane Mabey, additional, Kurbatova, Natalya, additional, Keays, Maria, additional, Kapushesky, Misha, additional, Gut, Marta, additional, Gut, Ivo, additional, Denning, David W., additional, and Bowyer, Paul, additional

Published
2017
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37. Laryngeal cyst of unusual origin and presentation

Author

Bochnia, Marek, Fraczek, Marcin, and Rabczynski, Jerzy

Subjects
Bronchial diseases -- Diagnosis, Bronchial diseases -- Care and treatment, Bronchial diseases -- Patient outcomes, Bronchial diseases -- Case studies, Laryngeal cancer -- Diagnosis, Laryngeal cancer -- Case studies, Health
Abstract

Branchial cysts are uncommon developmental anomalies rarely affecting the larynx. They arise mostly from the second branchial pouch, largely in the left anterior side of the neck. The peak incidence rate occurs in childhood. The most frequent clinical findings are voice disorders and respiratory distress of varying intensity. We describe a case of unusual presentation of IV branchial anomaly imitating a laryngeal cyst of typical epithelial origin. The lesion is reported also for its right-side location, advanced patient's age and long, uneventful history. The authors point out the need to consider also such a rare anomaly among other more frequent intralaryngeal lesions. Keywords: laryngeal cysts, fourth branchial cleft anomalies, Table of Contents Abstract Introduction Case Report Discussion References Introduction Laryngeal cysts are rare, mostly benign lesions affecting both sexes and all age groups. The symptoms depend on cyst localization [...]

Published
2008

38. Two cases of nasal neurofibroma

Author

Fraczek, Marcin, Zalesska-Krecicka, Maria, Zatonski, Tomasz, and Krecicki, Tomasz

Subjects
Neurofibroma -- Development and progression, Neurofibroma -- Case studies, Neurofibroma -- Care and treatment, Nose cancer -- Development and progression, Nose cancer -- Care and treatment, Nose cancer -- Case studies, Health
Abstract

Table of Contents Abstract Introduction Case Reports Discussion References Abstract We describe here two cases of neurofibroma arising from the nasal cavity. Those cases represent a peripheral nerve sheath tumor [...]

Published
2007

44. Coexistent chronic myelogenous leukemia with squamous cell carcinoma of the larynx associated with NOD2/CARD15 mutation in a young adult

Author

Fraczek, Marcin, Stembalska, Agnieszka, Karpinski, Pawel, and Krecicki, Tomasz

Subjects
Squamous cell carcinoma -- Case studies -- Diagnosis -- Care and treatment, Chronic myeloid leukemia -- Genetic aspects -- Case studies -- Diagnosis -- Care and treatment, Laryngeal cancer -- Case studies -- Diagnosis -- Care and treatment, Health
Abstract

We report the case of a 37-year-old man with human papillomavirus-positive squamous cell carcinoma of the larynx coexisting with chronic myelogenous leukemia. The patient had no history of smoking or [...]

Published
2016

45. Epidermal differentiation complex (locus 1q21) gene expression in head and neck cancer and normal mucosa

Author

Tyszkiewicz, Tomasz, primary, Jarzab, Michal, additional, Szymczyk, Cezary, additional, Kowal, Monika, additional, Krajewska, Jolanta, additional, Jaworska, Magdalena, additional, Fraczek, Marcin, additional, Krajewska, Anna, additional, Hadas, Ewa, additional, Swierniak, Michal, additional, Markowski, Jaroslaw, additional, Lange, Dariusz, additional, Poltorak, Stanislaw, additional, Wiench, Malgorzata, additional, Krecicki, Tomasz, additional, Jarzab, Jerzy, additional, and Maciejewski, Adam, additional

Published
2014
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49. Non-coding RNAs and disease: the classical ncRNAs make a comeback.

Author

Alves de Almeida, Rogerio, Fraczek, Marcin G., Parker, Steven, Delneri, Daniela, and O'Keefe, Raymond T.

Subjects
*NON-coding RNA, *CATALYTIC RNA, *HUMAN genome, *HUMAN chromosomes, *DISEASE management
Abstract

Many human diseases have been attributed tomutation in the protein coding regions of the human genome. The protein coding portion of the human genome, however, is very small compared with the non-coding portion of the genome. As such, there are a disproportionate number of diseases attributed to the coding compared with the non-coding portion of the genome. It is now clear that the non-coding portion of the genome produces many functional non-coding RNAs and these RNAs are slowly being linked to human diseases. Here we discuss examples where mutation in classical non-coding RNAs have been attributed to human disease and identify the future potential for the non-coding portion of the genome in disease biology. [ABSTRACT FROM AUTHOR]

Published
2016
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