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Oggenfuss U, Badet T, Croll D. A systematic screen for co-option of transposable elements across the fungal kingdom. Mob DNA 2024; 15:2. [PMID: 38245743 PMCID: PMC10799480 DOI: 10.1186/s13100-024-00312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived from Academ, Kolobok or Helitron. We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of putative host-TE fusions and facilitates systematic investigations of candidate fusion proteins.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Department of Microbiology and Immunology, University of Minnesota, Medical School, Minneapolis, Minnesota, United States of America
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
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Gierlicka I, Kasprzyk I, Wnuk M. Imaging Flow Cytometry as a Quick and Effective Identification Technique of Pollen Grains from Betulaceae, Oleaceae, Urticaceae and Asteraceae. Cells 2022; 11:cells11040598. [PMID: 35203248 PMCID: PMC8870286 DOI: 10.3390/cells11040598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 02/01/2023] Open
Abstract
Despite the continuous and intensive development of laboratory techniques, a light microscope is still the most common tool used in pollen grains differentiation. However, microscopy is time-consuming and needs well-educated and experienced researchers. Other currently used techniques can be categorised as images and non-images analysis, but each has certain limitations. We propose a new approach to differentiate pollen grains using the Imaging Flow Cytometry (IFC) technique. It allows for high-throughput fluorescence data recording, which, in contrast to the standard FC, also enables real-time control of the results thanks to the possibility of digital image recording of cells flowing through the measuring capillary. The developed method allows us to determine the characteristics of the pollen grains population based on the obtained fluorescence data, using various combinations of parameters available in the IDEAS software, which can be analysed on different fluorescence channels. On this basis, we distinguished pollen grains both between and within different genera belonging to the Betulaceae, Oleaceae, Urticaceae and Asteraceae families. Thereby, we prove that the proposed methodology is sufficient for accurate, fast, and cost-effective identification and potentially can be used in the routine analysis of allergenic pollen grains.
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Affiliation(s)
- Iwona Gierlicka
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland; (I.G.); (I.K.)
| | - Idalia Kasprzyk
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland; (I.G.); (I.K.)
| | - Maciej Wnuk
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
- Correspondence: ; Tel.: +48-17-851-86-09
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Unveiling E2F4, TEAD1 and AP-1 as regulatory transcription factors of the replicative senescence program by multi-omics analysis. Protein Cell 2022; 13:742-759. [PMID: 35023014 PMCID: PMC9233726 DOI: 10.1007/s13238-021-00894-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/26/2021] [Indexed: 01/10/2023] Open
Abstract
Senescence, a stable state of growth arrest, affects many physiological and pathophysiological processes, especially aging. Previous work has indicated that transcription factors (TFs) play a role in regulating senescence. However, a systematic study of regulatory TFs during replicative senescence (RS) using multi-omics analysis is still lacking. Here, we generated time-resolved RNA-seq, reduced representation bisulfite sequencing (RRBS) and ATAC-seq datasets during RS of mouse skin fibroblasts, which demonstrated that an enhanced inflammatory response and reduced proliferative capacity were the main characteristics of RS in both the transcriptome and epigenome. Through integrative analysis and genetic manipulations, we found that transcription factors E2F4, TEAD1 and AP-1 are key regulators of RS. Overexpression of E2f4 improved cellular proliferative capacity, attenuated SA-β-Gal activity and changed RS-associated differentially methylated sites (DMSs). Moreover, knockdown of Tead1 attenuated SA-β-Gal activity and partially altered the RS-associated transcriptome. In addition, knockdown of Atf3, one member of AP-1 superfamily TFs, reduced Cdkn2a (p16) expression in pre-senescent fibroblasts. Taken together, the results of this study identified transcription factors regulating the senescence program through multi-omics analysis, providing potential therapeutic targets for anti-aging.
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Ciurea CN, Kosovski IB, Mare AD, Toma F, Pintea-Simon IA, Man A. Candida and Candidiasis-Opportunism Versus Pathogenicity: A Review of the Virulence Traits. Microorganisms 2020; 8:microorganisms8060857. [PMID: 32517179 PMCID: PMC7355540 DOI: 10.3390/microorganisms8060857] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022] Open
Abstract
One of the most important questions in microbiology nowadays, is how apparently harmless, commensal yeasts like Candida spp. can cause a rising number of infections. The occurrence of the disease requires firstly the attachment to the host cells, followed by the invasion of the tissue. The adaptability translates into a rapid ability to respond to stress factors, to take up nutrients or to multiply under different conditions. By forming complex intracellular networks such as biofilms, Candida spp. become not only more refractive to antifungal therapies but also more prone to cause disease. The inter-microbial interactions can enhance the virulence of a strain. In vivo, the fungal cells face a multitude of challenges and, as a result, they develop complex strategies serving one ultimate goal: survival. This review presents the virulence factors of the most important Candida spp., contributing to a better understanding of the onset of candidiasis and raising awareness of the highly complex interspecies interactions that can change the outcome of the disease.
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Affiliation(s)
- Cristina Nicoleta Ciurea
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania; (A.D.M.); (F.T.); (I.A.P.-S.); (A.M.)
- Doctoral School, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania;
- Correspondence:
| | - Irina-Bianca Kosovski
- Doctoral School, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania;
- Department of Physiopathology, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania
| | - Anca Delia Mare
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania; (A.D.M.); (F.T.); (I.A.P.-S.); (A.M.)
| | - Felicia Toma
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania; (A.D.M.); (F.T.); (I.A.P.-S.); (A.M.)
| | - Ionela Anca Pintea-Simon
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania; (A.D.M.); (F.T.); (I.A.P.-S.); (A.M.)
- Doctoral School, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania;
| | - Adrian Man
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania; (A.D.M.); (F.T.); (I.A.P.-S.); (A.M.)
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