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Fernandes JAL, Zatti MDS, Arantes TD, de Souza MFB, Santoni MM, Rossi D, Zanelli CF, Liu XQ, Bagagli E, Theodoro RC. Cryptococcus neoformans Prp8 Intein: An In Vivo Target-Based Drug Screening System in Saccharomyces cerevisiae to Identify Protein Splicing Inhibitors and Explore Its Dynamics. J Fungi (Basel) 2022; 8:jof8080846. [PMID: 36012834 PMCID: PMC9410109 DOI: 10.3390/jof8080846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022] Open
Abstract
Inteins are genetic mobile elements that are inserted within protein-coding genes, which are usually housekeeping genes. They are transcribed and translated along with the host gene, then catalyze their own splicing out of the host protein, which assumes its functional conformation thereafter. As Prp8 inteins are found in several important fungal pathogens and are absent in mammals, they are considered potential therapeutic targets since inhibiting their splicing would selectively block the maturation of fungal proteins. We developed a target-based drug screening system to evaluate the splicing of Prp8 intein from the yeast pathogen Cryptococcus neoformans (CnePrp8i) using Saccharomyces cerevisiae Ura3 as a non-native host protein. In our heterologous system, intein splicing preserved the full functionality of Ura3. To validate the system for drug screening, we examined cisplatin, which has been described as an intein splicing inhibitor. By using our system, new potential protein splicing inhibitors may be identified and used, in the future, as a new class of drugs for mycosis treatment. Our system also greatly facilitates the visualization of CnePrp8i splicing dynamics in vivo.
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Affiliation(s)
- José Alex Lourenço Fernandes
- Institute of Tropical Medicine, Federal University of Rio Grande do Norte (UFRN), Natal 59077-080, Rio Grande do Norte, Brazil
- Department of Biochemistry, Biosciences Center, Federal University of Rio Grande do Norte (UFRN), Natal 59078-900, Rio Grande do Norte, Brazil
- Ottawa Hospital Research Institute (OHRI), The University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Correspondence: (J.A.L.F.); (R.C.T.)
| | - Matheus da Silva Zatti
- Institute of Tropical Medicine, Federal University of Rio Grande do Norte (UFRN), Natal 59077-080, Rio Grande do Norte, Brazil
- Department of Biochemistry, Biosciences Center, Federal University of Rio Grande do Norte (UFRN), Natal 59078-900, Rio Grande do Norte, Brazil
| | - Thales Domingos Arantes
- Department of Biosciences and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia 74605-050, Goiás, Brazil
| | - Maria Fernanda Bezerra de Souza
- Department of Biochemistry, Biosciences Center, Federal University of Rio Grande do Norte (UFRN), Natal 59078-900, Rio Grande do Norte, Brazil
| | - Mariana Marchi Santoni
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, São Paulo, Brazil
| | - Danuza Rossi
- Pensabio, São Paulo 05005-010, São Paulo, Brazil
| | - Cleslei Fernando Zanelli
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, São Paulo, Brazil
| | - Xiang-Qin Liu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Eduardo Bagagli
- Microbiology and Immunology Department, Biosciences Institute of Botucatu, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil
| | - Raquel Cordeiro Theodoro
- Institute of Tropical Medicine, Federal University of Rio Grande do Norte (UFRN), Natal 59077-080, Rio Grande do Norte, Brazil
- Correspondence: (J.A.L.F.); (R.C.T.)
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Tharappel AM, Li Z, Li H. Inteins as Drug Targets and Therapeutic Tools. Front Mol Biosci 2022; 9:821146. [PMID: 35211511 PMCID: PMC8861304 DOI: 10.3389/fmolb.2022.821146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Multidrug-resistant pathogens are of significant concern in recent years. Hence new antifungal and anti-bacterial drug targets are urgently needed before the situation goes beyond control. Inteins are polypeptides that self-splice from exteins without the need for cofactors or external energy, resulting in joining of extein fragments. Inteins are present in many organisms, including human pathogens such as Mycobacterium tuberculosis, Cryptococcus neoformans, C. gattii, and Aspergillus fumigatus. Because intein elements are not present in human genes, they are attractive drug targets to develop antifungals and antibiotics. Thus far, a few inhibitors of intein splicing have been reported. Metal-ions such as Zn2+ and Cu2+, and platinum-containing compound cisplatin inhibit intein splicing in M. tuberculosis and C. neoformans by binding to the active site cysteines. A small-molecule inhibitor 6G-318S and its derivative 6G-319S are found to inhibit intein splicing in C. neoformans and C. gattii with a MIC in nanomolar concentrations. Inteins have also been used in many other applications. Intein can be used in activating a protein inside a cell using small molecules. Moreover, split intein can be used to deliver large genes in experimental gene therapy and to kill selected species in a mixed population of microbes by taking advantage of the toxin-antitoxin system. Furthermore, split inteins are used in synthesizing cyclic peptides and in developing cell culture model to study infectious viruses including SARS-CoV-2 in the biosafety level (BSL) 2 facility. This mini-review discusses the recent research developments of inteins in drug discovery and therapeutic research.
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Affiliation(s)
- Anil Mathew Tharappel
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
- *Correspondence: Hongmin Li,
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Garcia Garces H, Hamae Yamauchi D, Theodoro RC, Bagagli E. PRP8 Intein in Onygenales: Distribution and Phylogenetic Aspects. Mycopathologia 2019; 185:37-49. [PMID: 31286362 DOI: 10.1007/s11046-019-00355-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/27/2019] [Indexed: 11/30/2022]
Abstract
Inteins (internal proteins) are mobile genetic elements, inserted in housekeeping proteins, with self-splicing properties. Some of these elements have been recently pointed out as modulators of genetic expression or protein function. Herein, we evaluated, in silico, the distribution and phylogenetic patterns of PRP8 intein among 93 fungal strains of the order Onygenales. PRP8 intein(s) are present in most of the species (45/49), mainly as full-length inteins (containing both the Splicing and the Homing Endonuclease domains), and must have transferred vertically in all lineages, since their phylogeny reflects the group phylogeny. While the distribution of PRP8 intein(s) varies among species of Onygenaceae family, being absent in Coccidioides spp. and present as full and mini-intein in other species, they are consistently observed as full-length inteins in all evaluated pathogenic species of the Arthrodermataceae and Ajellomycetaceae families. This conservative and massive PRP8 intein presence in Ajellomycetacean and Arthrodermatecean species reinforces the previous idea that such genetic elements do not decrease the fungal fitness significantly and even might play some role in the host-pathogen relationship, at least in these two fungal groups. We may better position the species Ophidiomyces ophiodiicola (with no intein) in the Onygenaceae family and Onygena corvina (with a full-length intein) as a basal member in the Arthrodermataceae family.
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Affiliation(s)
- Hans Garcia Garces
- Microbiology and Immunology Department, Biosciences Institute of Botucatu, State University of Sao Paulo (UNESP), Botucatu, São Paulo, Brazil
| | - Danielle Hamae Yamauchi
- Microbiology and Immunology Department, Biosciences Institute of Botucatu, State University of Sao Paulo (UNESP), Botucatu, São Paulo, Brazil
| | - Raquel Cordeiro Theodoro
- Tropical Medicine Institute of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Eduardo Bagagli
- Microbiology and Immunology Department, Biosciences Institute of Botucatu, State University of Sao Paulo (UNESP), Botucatu, São Paulo, Brazil.
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Garcia Garces H, Cordeiro RT, Bagagli E. PRP8 intein in dermatophytes: Evolution and species identification. Med Mycol 2018; 56:746-758. [PMID: 29228309 DOI: 10.1093/mmy/myx102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/27/2017] [Indexed: 11/14/2022] Open
Abstract
Dermatophytes are keratinophilic fungi belonging to the family Arthrodermataceae. Despite having a monophyletic origin, its systematics has always been complex and controversial. Sequencing of nuclear ribosomal ITS and D1/D2 rDNA has been proposed as an efficient tool for identifying species in this group of fungi, while multilocus analyses have been used for phylogenetic species recognition. However, the search for new markers, with sequence and size variation, which enable species identification in only one polymerase chain reaction (PCR) step, is very attractive. Inteins seems to fulfill these characteristics. They are self-splicing genetic elements present within housekeeping coding genes, such as PRP8, that codify the most important protein of the spliceosome. The PRP8 intein has been described for Microsporum canis in databases but has not been studied in dermatophytes in any other published work. Thus, our aim was to determine the potential of this intervening element for establishing phylogenetic relationships among dermatophytes and for identifying species. It was found that all studied species have a full-length PRP8 intein with a Homing Endonuclease belonging to the family LAGLIDADG. Phylogenetic analyses were consistent with other previous phylogenies, confirming Epidermophyton floccosum in the same clade of the Arthroderma gypseum complex, Microsporum audouinii close to M. canis, differentiating A. gypseum from Arthroderma incurvatum, and in addition, better defining the Trichophyton interdigitale and Trichophyton rubrum species grouping. Length polymorphism in the HE region enables identification of the most relevant Microsporum species by a simple PCR-electrophoresis assay. Intein PRP8 within dermatophytes is a powerful additional tool for identifying and systematizing dermatophytes.
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Affiliation(s)
- Hans Garcia Garces
- Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual de São Paulo. São Paulo. Brasil
| | - Raquel Theodoro Cordeiro
- Instituto de Medicina Tropical do RN, Universidade Federal de Rio Grande do Norte. Rio Grande do Norte. Brasil
| | - E Bagagli
- Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual de São Paulo. São Paulo. Brasil
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Fernandes JAL, Prandini THR, Castro MDCA, Arantes TD, Giacobino J, Bagagli E, Theodoro RC. Evolution and Application of Inteins in Candida species: A Review. Front Microbiol 2016; 7:1585. [PMID: 27777569 PMCID: PMC5056185 DOI: 10.3389/fmicb.2016.01585] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/21/2016] [Indexed: 11/13/2022] Open
Abstract
Inteins are invasive intervening sequences that perform an autocatalytic splicing from their host proteins. Among eukaryotes, these elements are present in many fungal species, including those considered opportunistic or primary pathogens, such as Candida spp. Here we reviewed and updated the list of Candida species containing inteins in the genes VMA, THRRS and GLT1 and pointed out the importance of these elements as molecular markers for molecular epidemiological researches and species-specific diagnosis, since the presence, as well as the size of these inteins, is polymorphic among the different species. Although absent in Candida albicans, these elements are present in different sizes, in some environmental Candida spp. and also in most of the non-albicans Candida spp. considered emergent opportunistic pathogens. Besides, the possible role of these inteins in yeast physiology was also discussed in the light of the recent findings on the importance of these elements as post-translational modulators of gene expression, reinforcing their relevance as alternative therapeutic targets for the treatment of non-albicans Candida infections, because, once the splicing of an intein is inhibited, its host protein, which is usually a housekeeping protein, becomes non-functional.
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Affiliation(s)
- José A L Fernandes
- Institute of Tropical Medicine of Rio Grande do Norte, Universidade Federal do Rio Grande do Norte Natal, Brazil
| | - Tâmara H R Prandini
- Department of Microbiology and Immunology, Institute of Biosciences, Universidade Estadual Paulista Julio de Mesquita Filho Botucatu, Brazil
| | - Maria da Conceiçao A Castro
- Institute of Tropical Medicine of Rio Grande do Norte, Universidade Federal do Rio Grande do Norte Natal, Brazil
| | - Thales D Arantes
- Institute of Tropical Medicine of Rio Grande do Norte, Universidade Federal do Rio Grande do NorteNatal, Brazil; Post-graduation Program in Biochemistry, Universidade Federal do Rio Grande do NorteNatal, Brazil
| | - Juliana Giacobino
- Department of Microbiology and Immunology, Institute of Biosciences, Universidade Estadual Paulista Julio de Mesquita Filho Botucatu, Brazil
| | - Eduardo Bagagli
- Department of Microbiology and Immunology, Institute of Biosciences, Universidade Estadual Paulista Julio de Mesquita Filho Botucatu, Brazil
| | - Raquel C Theodoro
- Institute of Tropical Medicine of Rio Grande do Norte, Universidade Federal do Rio Grande do Norte Natal, Brazil
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PRP8 intein in cryptic species of Histoplasma capsulatum: evolution and phylogeny. INFECTION GENETICS AND EVOLUTION 2013; 18:174-82. [PMID: 23665464 DOI: 10.1016/j.meegid.2013.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/12/2013] [Accepted: 05/01/2013] [Indexed: 02/03/2023]
Abstract
The PRP8 intein is the most widespread intein among the Kingdom Fungi. This genetic element occurs within the prp8 gene, and is transcribed and translated simultaneously with the gene. After translation, the intein excises itself from the Prp8 protein by an autocatalytic splicing reaction, subsequently joining the N and C terminals of the host protein, which retains its functional conformation. Besides the splicing domain, some PRP8 inteins also have a homing endonuclease (HE) domain which, if functional, makes the intein a mobile element capable of becoming fixed in a population. This work aimed to study (1) The occurrence of this intein in Histoplasma capsulatum isolates (n=99) belonging to different cryptic species collected in diverse geographical locations, and (2) The functionality of the endonuclease domains of H. capsulatum PRP8 inteins and their phylogenetic relationship among the cryptic species. Our results suggest that the PRP8 intein is fixed in H. capsulatum populations and that an admixture or a probable ancestral polymorphism of the PRP8 intein sequences is responsible for the apparent paraphyletic pattern of the LAmA clade which, in the intein phylogeny, also encompasses sequences from LAmB isolates. The PRP8 intein sequences clearly separate the different cryptic species, and may serve as an additional molecular typing tool, as previously proposed for other fungi genus, such as Cryptococcus and Paracoccidioides.
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Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis. PLoS One 2012; 7:e35750. [PMID: 22563396 PMCID: PMC3338533 DOI: 10.1371/journal.pone.0035750] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 03/24/2012] [Indexed: 01/09/2023] Open
Abstract
Candida orthopsilosis is closely related to the fungal pathogen Candida parapsilosis. However, whereas C. parapsilosis is a major cause of disease in immunosuppressed individuals and in premature neonates, C. orthopsilosis is more rarely associated with infection. We sequenced the C. orthopsilosis genome to facilitate the identification of genes associated with virulence. Here, we report the de novo assembly and annotation of the genome of a Type 2 isolate of C. orthopsilosis. The sequence was obtained by combining data from next generation sequencing (454 Life Sciences and Illumina) with paired-end Sanger reads from a fosmid library. The final assembly contains 12.6 Mb on 8 chromosomes. The genome was annotated using an automated pipeline based on comparative analysis of genomes of Candida species, together with manual identification of introns. We identified 5700 protein-coding genes in C. orthopsilosis, of which 5570 have an ortholog in C. parapsilosis. The time of divergence between C. orthopsilosis and C. parapsilosis is estimated to be twice as great as that between Candida albicans and Candida dubliniensis. There has been an expansion of the Hyr/Iff family of cell wall genes and the JEN family of monocarboxylic transporters in C. parapsilosis relative to C. orthopsilosis. We identified one gene from a Maltose/Galactoside O-acetyltransferase family that originated by horizontal gene transfer from a bacterium to the common ancestor of C. orthopsilosis and C. parapsilosis. We report that TFB3, a component of the general transcription factor TFIIH, undergoes alternative splicing by intron retention in multiple Candida species. We also show that an intein in the vacuolar ATPase gene VMA1 is present in C. orthopsilosis but not C. parapsilosis, and has a patchy distribution in Candida species. Our results suggest that the difference in virulence between C. parapsilosis and C. orthopsilosis may be associated with expansion of gene families.
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Ramsden R, Arms L, Davis TN, Muller EGD. An intein with genetically selectable markers provides a new approach to internally label proteins with GFP. BMC Biotechnol 2011; 11:71. [PMID: 21708017 PMCID: PMC3141402 DOI: 10.1186/1472-6750-11-71] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/27/2011] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Inteins are proteins that catalyze their own removal from within larger precursor proteins. In the process they splice the flanking protein sequences, termed the N-and C-terminal exteins. Large inteins frequently have a homing endonuclease that is involved in maintaining the intein in the host. Splicing and nuclease activity are independent and distinct domains in the folded structure. We show here that other biochemical activities can be incorporated into an intein in place of the endonuclease without affecting splicing and that these activities can provide genetic selection for the intein. We have coupled such a genetically marked intein with GFP as the N-terminal extein to create a cassette to introduce GFP within the interior of a targeted protein. RESULTS The Pch PRP8 mini-intein of Penicillium chrysogenum was modified to include: 1) aminoglycoside phosphotransferase; 2) imidazoleglycerol-phosphate dehydratase, His5 from S. pombe ; 3) hygromycin B phosphotransferase; and 4) the transcriptional activator LexA-VP16. The proteins were inserted at the site of the lost endonuclease. When expressed in E. coli, all of the modified inteins spliced at high efficiency. Splicing efficiency was also greater than 96% when expressed from a plasmid in S. cerevisiae. In addition the inteins conferred either G418 or hygromycin resistance, or histidine or leucine prototropy, depending on the inserted marker and the yeast genetic background. DNA encoding the marked inteins coupled to GFP as the N-terminal extein was PCR amplified with ends homologous to an internal site in the yeast calmodulin gene CMD1. The DNA was transformed into yeast and integrants obtained by direct selection for the intein's marker. The His5-marked intein yielded a fully functional calmodulin that was tagged with GFP within its central linker. CONCLUSIONS Inteins continue to show their flexibility as tools in molecular biology. The Pch PRP8 intein can successfully tolerate a variety of genetic markers and still retain high splicing efficiency. We have shown that a genetically marked intein can be used to insert GFP in one-step within a target protein in vivo.
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Affiliation(s)
- Richard Ramsden
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Luther Arms
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Eric GD Muller
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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