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Lietard J, Ameur D, Damha MJ, Somoza MM. High-Density RNA Microarrays Synthesized In Situ by Photolithography. Angew Chem Int Ed Engl 2018; 57:15257-15261. [PMID: 30187993 PMCID: PMC6237118 DOI: 10.1002/anie.201806895] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Indexed: 02/03/2023]
Abstract
While high-density DNA microarrays have been available for over three decades, the synthesis of equivalent RNA microarrays has proven intractable until now. Herein we describe the first in situ synthesis of mixed-based, high-density RNA microarrays using photolithography and light-sensitive RNA phosphoramidites. With coupling efficiencies comparable to those of DNA monomers, RNA oligonucleotides at least 30 nucleotides long can now efficiently be prepared using modified phosphoramidite chemistry. A two-step deprotection route unmasks the phosphodiester, the exocyclic amines and the 2' hydroxyl. Hybridization and enzymatic assays validate the quality and the identity of the surface-bound RNA. We show that high-density is feasible by synthesizing a complex RNA permutation library with 262144 unique sequences. We also introduce DNA/RNA chimeric microarrays and explore their applications by mapping the sequence specificity of RNase HII.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Dominik Ameur
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Masad J. Damha
- Department of ChemistryMcGill University801 Rue Sherbrooke OMontréalQC H3A 0B8Canada
| | - Mark M. Somoza
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
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Lietard J, Ameur D, Damha MJ, Somoza MM. In‐situ‐Synthese von hochdichten RNA‐Mikroarrays mittels Photolithographie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jory Lietard
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
| | - Dominik Ameur
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
| | - Masad J. Damha
- Department of ChemistryMcGill University 801 Rue Sherbrooke O Montréal QC H3A 0B8 Kanada
| | - Mark M. Somoza
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
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Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete. PLoS Genet 2016; 12:e1006110. [PMID: 27327578 PMCID: PMC4915694 DOI: 10.1371/journal.pgen.1006110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/16/2016] [Indexed: 11/19/2022] Open
Abstract
In fungi belonging to the phylum Basidiomycota, sexual compatibility is usually determined by two genetically unlinked MAT loci, one of which encodes one or more pheromone receptors (P/R) and pheromone precursors, and the other comprehends at least one pair of divergently transcribed genes encoding homeodomain (HD) transcription factors. Most species are heterothallic, meaning that sexual reproduction requires mating between two sexually compatible individuals harboring different alleles at both MAT loci. However, some species are known to be homothallic, one individual being capable of completing the sexual cycle without mating with a genetically distinct partner. While the molecular underpinnings of the heterothallic life cycles of several basidiomycete model species have been dissected in great detail, much less is known concerning the molecular basis for homothallism. Following the discovery in available draft genomes of the homothallic basidiomycetous yeast Phaffia rhodozyma of P/R and HD genes, we employed available genetic tools to determine their role in sexual development. Two P/R clusters, each harboring one pheromone receptor and one pheromone precursor gene were found in close vicinity of each other and were shown to form two redundant P/R pairs, each receptor being activated by the pheromone encoded by the most distal pheromone precursor gene. The HD locus is apparently genetically unlinked to the P/R locus and encodes a single pair of divergently transcribed HD1 and HD2 transcription factors, both required for normal completion of the sexual cycle. Given the genetic makeup of P. rhodozyma MAT loci, we postulate that it is a primarily homothallic organism and we propose a model for the interplay of molecular interactions required for sexual development in this species. Phaffia rhodozyma is considered one of the most promising microbial source of the carotenoid astaxanthin. Further development of this yeast as an industrial organism will benefit from new insights regarding its sexual reproduction system. Some fungi are capable of sexual reproduction without the need for a sexually compatible partner, a behavior called homothallism. For some of these fungi, it was observed that they carried in a single individual all the genes normally determining sexual identity in two distinct sexually compatible individuals, but in most cases the role of these genes is still unclear. Here we examined in detail the homothallic sexual cycle of the yeast Phaffia rhodozyma that belongs to the Basidiomycota, which is the fungal lineage that also includes the mushrooms. Phaffia rhodozyma produces astaxanthin, a pigment with antioxidant properties used in the food and cosmetic industries and is accessible to genetic modifications, so far aimed mainly at improving astaxanthin production. Here we harnessed these genetic tools to dissect the self-fertile life cycle of this yeast and found that all genes normally involved in two-partner sexual reproduction are also required for self-fertile sex in P. rhodozyma and propose a model describing molecular interactions required to trigger sexual development. We also generated preferably outcrossing strains, which are potentially useful for further improvement of P. rhodozyma as an industrial organism.
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Mead ME, Stanton BC, Kruzel EK, Hull CM. Targets of the Sex Inducer homeodomain proteins are required for fungal development and virulence in Cryptococcus neoformans. Mol Microbiol 2015; 95:804-18. [PMID: 25476490 PMCID: PMC4339537 DOI: 10.1111/mmi.12898] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2014] [Indexed: 01/14/2023]
Abstract
In the yeast Saccharomyces cerevisiae, the regulation of cell types by homeodomain transcription factors is a key paradigm; however, many questions remain regarding this class of developmental regulators in other fungi. In the human fungal pathogen Cryptococcus neoformans, the homeodomain transcription factors Sxi1α and Sxi2a are required for sexual development that produces infectious spores, but the molecular mechanisms by which they drive this process are unknown. To better understand homeodomain control of fungal development, we determined the targets of the Sxi2a-Sxi1α heterodimer using whole genome expression analyses paired with in silico and in vitro binding site identification methods. We identified Sxi-regulated genes that contained a site bound directly by the Sxi proteins that is required for full regulation in vivo. Among the targets of the Sxi2a-Sxi1α complex were many genes known to be involved in sexual reproduction, as well as several well-studied virulence genes. Our findings suggest that genes involved in sexual development are also important in mammalian disease. Our work advances the understanding of how homeodomain transcription factors control complex developmental events and suggests an intimate link between fungal development and virulence.
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Affiliation(s)
- Matthew E Mead
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53706, USA
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Stanton BC, Nielsen AAK, Tamsir A, Clancy K, Peterson T, Voigt CA. Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat Chem Biol 2014; 10:99-105. [PMID: 24316737 PMCID: PMC4165527 DOI: 10.1038/nchembio.1411] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/30/2013] [Indexed: 01/25/2023]
Abstract
Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply 'part mining' to build a library of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset were determined using an in vitro method, and this information was used to build synthetic promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 were identified that both strongly repress their cognate promoter (5- to 207-fold) and exhibit minimal interactions with other promoters. Each repressor-promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOT/NOR gates, there are >10(54) circuits that could be built by changing the pattern of input and output promoters. This represents a large set of compatible gates that can be used to construct user-defined circuits.
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Affiliation(s)
- Brynne C Stanton
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alec A K Nielsen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alvin Tamsir
- Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California, USA
| | - Kevin Clancy
- Synthetic Biology R&D Unit, Life Technologies, Carlsbad, California, USA
| | - Todd Peterson
- Synthetic Biology R&D Unit, Life Technologies, Carlsbad, California, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Au CH, Wong MC, Bao D, Zhang M, Song C, Song W, Law PTW, Kües U, Kwan HS. The genetic structure of the A mating-type locus of Lentinula edodes. Gene 2013; 535:184-90. [PMID: 24295887 DOI: 10.1016/j.gene.2013.11.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 11/14/2013] [Accepted: 11/16/2013] [Indexed: 11/29/2022]
Abstract
The Shiitake mushroom, Lentinula edodes (Berk.) Pegler is a tetrapolar basidiomycete with two unlinked mating-type loci, commonly called the A and B loci. Identifying the mating-types in shiitake is important for enhancing the breeding and cultivation of this economically-important edible mushroom. Here, we identified the A mating-type locus from the first draft genome sequence of L. edodes and characterized multiple alleles from different monokaryotic strains. Two intron-length polymorphism markers were developed to facilitate rapid molecular determination of A mating-type. L. edodes sequences were compared with those of known tetrapolar and bipolar basidiomycete species. The A mating-type genes are conserved at the homeodomain region across the order Agaricales. However, we observed unique genomic organization of the locus in L. edodes which exhibits atypical gene order and multiple repetitive elements around its A locus. To our knowledge, this is the first known exception among Homobasidiomycetes, in which the mitochondrial intermediate peptidase (mip) gene is not closely linked to A locus.
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Affiliation(s)
- Chun Hang Au
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Man Chun Wong
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Dapeng Bao
- Edible Fungi Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Meiyan Zhang
- Edible Fungi Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chunyan Song
- Edible Fungi Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wenhua Song
- Edible Fungi Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Patrick Tik Wan Law
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ursula Kües
- Division of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Hoi Shan Kwan
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Abstract
The ability of fungi to transition between unicellular and multicellular growth has a profound impact on our health and the economy. Many important fungal pathogens of humans, animals, and plants are dimorphic, and the ability to switch between morphological states has been associated with their virulence. Cryptococcus neoformans is a human fungal pathogen that causes life-threatening meningoencephalitis in immunocompromised and, in some cases, immunocompetent hosts. Cryptococcus neoformans grows vegetatively as a budding yeast and switches to hyphal growth during the sexual cycle, which is important in the study of cryptococcal pathogenicity because spores resulting from sexual development are infectious propagules and can colonize the lungs of a host. In addition, sexual reproduction contributes to the genotypic variability of Cryptococcus species, which may lead to increased fitness and virulence. Despite significant advances in our understanding of the mechanisms behind the development of C. neoformans, our knowledge is still incomplete. Recent studies have led to the emergence of many intriguing questions and hypotheses. In this review, we describe and discuss the most interesting aspects of C. neoformans development and address their impact on pathogenicity.
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Affiliation(s)
- Lukasz Kozubowski
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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Kruzel EK, Hull CM. Establishing an unusual cell type: how to make a dikaryon. Curr Opin Microbiol 2010; 13:706-11. [PMID: 21036099 DOI: 10.1016/j.mib.2010.09.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 09/25/2010] [Accepted: 09/28/2010] [Indexed: 12/19/2022]
Abstract
The dikaryons of basidiomycete fungi represent an unusual cell type required for complete sexual development. Dikaryon formation occurs via the activities of cell type-specific homeodomain transcription factors, which form regulatory complexes to establish the dikaryotic state. Decades of classical genetic and cell biological studies in mushrooms have provided a foundation for more recent molecular studies in the pathogenic species Ustilago maydis and Cryptococcus neoformans. Studies in these systems have revealed novel mechanisms of regulation that function downstream of classic homeodomain complexes to ensure that dikaryons are established and propagated. Comparisons of these dikaryon-specific networks promise to reveal the nature of regulatory network evolution and the adaptations responsible for driving complex eukaryotic development.
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Affiliation(s)
- Emilia K Kruzel
- Department of Biomolecular Chemistry, University of Wisconsin, School of Medicine and Public Health, Madison, WI 53706, United States
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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