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Schneider RF, Hallstrom K, DeMott C, McDonough KA. Conditional protein splicing of the Mycobacterium tuberculosis RecA intein in its native host. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589443. [PMID: 38659745 PMCID: PMC11042385 DOI: 10.1101/2024.04.15.589443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The recA gene, encoding Recombinase A (RecA) is one of three Mycobacterium tuberculosis (Mtb) genes encoding an in-frame intervening protein sequence (intein) that must splice out of precursor host protein to produce functional protein. Ongoing debate about whether inteins function solely as selfish genetic elements or benefit their host cells requires understanding of interplay between inteins and their hosts. We measured environmental effects on native RecA intein splicing within Mtb using a combination of western blots and promoter reporter assays. RecA splicing was stimulated in bacteria exposed to DNA damaging agents or by treatment with copper in hypoxic, but not normoxic, conditions. Spliced RecA was processed by the Mtb proteasome, while free intein was degraded efficiently by other unknown mechanisms. Unspliced precursor protein was not observed within Mtb despite its accumulation during ectopic expression of Mtb recA within E. coli. Surprisingly, Mtb produced free N-extein in some conditions, and ectopic expression of Mtb N-extein activated LexA in E. coli. These results demonstrate that the bacterial environment greatly impacts RecA splicing in Mtb, underscoring the importance of studying intein splicing in native host environments and raising the exciting possibility of intein splicing as a novel regulatory mechanism in Mtb.
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Affiliation(s)
- Ryan F. Schneider
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany
| | | | | | - Kathleen A. McDonough
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany
- Wadsworth Center, New York Department of Health
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Panda S, Rout M, Mishra S, Turuk J, Pati S, Dehury B. Molecular docking and MD simulations reveal protease inhibitors block the catalytic residues in Prp8 intein of Aspergillus fumigatus: a potential target for antimycotics. J Biomol Struct Dyn 2023:1-16. [PMID: 38149850 DOI: 10.1080/07391102.2023.2298735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 12/28/2023]
Abstract
Resistance to azoles and amphotericin B especially in Aspergillus fumigatus is a growing concern towards the treatment of invasive fungal infection. At this critical juncture, intein splicing would be a productive, and innovative target to establish therapies against resistant strains. Intein splicing is the central event for the activation of host protein, essential for the growth and survival of various microorganisms including A. fumigatus. The splicing process is a four-step protease-like nucleophilic cascade. Thus, we hypothesise that protease inhibitors would successfully halt intein splicing and potentially restrict the growth of the aforementioned pathogen. Using Rosetta Fold and molecular dynamics simulations, we modelled Prp8 intein structure; resembling classic intein fold with horse shoe shaped splicing domain. To fully comprehend the active site of Afu Prp8 intein, C1, T62, H65, H818, N819 from intein sequences and S820, the first C-extein residue are selected. Molecular docking shows that two FDA-approved drugs, i.e. Lufotrelvir and Remdesivir triphosphate efficiently interact with Prp8 intein from the assortment of 212 protease inhibitors. MD simulation portrayed that Prp8 undergoes conformational change upon ligand binding, and inferred the molecular recognition and stability of the docked complexes. Per-residue decomposition analysis confirms the importance of F: block R802, V803, and Q807 binding pocket in intein splicing domain towards recognition of inhibitors, along with active site residues through strong hydrogen bonds and hydrophobic contacts. However, in vitro and in vivo assays are required to confirm the inhibitory action on Prp8 intein splicing; which may pave the way for the development of new antifungals for A. fumigatus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Jyotirmayee Turuk
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sanghamitra Pati
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
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Tharappel AM, Li Z, Zhu YC, Wu X, Chaturvedi S, Zhang QY, Li H. Calcimycin Inhibits Cryptococcus neoformans In Vitro and In Vivo by Targeting the Prp8 Intein Splicing. ACS Infect Dis 2022; 8:1851-1868. [PMID: 35948057 PMCID: PMC9464717 DOI: 10.1021/acsinfecdis.2c00137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Drug resistance is a significant concern in the treatment of diseases, including cryptococcosis caused by Cryptococcus neoformans (Cne) and Cryptococcus gattii (Cga). Alternative drug targets are necessary to overcome drug resistance before it attains a critical stage. Splicing of inteins from pro-protein precursors is crucial for activities of essential proteins hosting intein elements in many organisms, including human pathogens such as Cne and Cga. Through a high-throughput screening, we identified calcimycin (CMN) as a potent Prp8 intein splicing inhibitor with a minimum inhibitory concentration (MIC) of 1.5 μg/mL against the wild-type Cne-H99 (Cne-WT or Cne). In contrast, CMN inhibited the intein-less mutant strain (Cne-Mut) with a 16-fold higher MIC. Interestingly, Aspergillus fumigatus and a few Candida species were resistant to CMN. Further studies indicated that CMN reduced virulence factors such as urease activity, melanin production, and biofilm formation in Cne. CMN also inhibited Cne intracellular infection in macrophages. In a target-specific split nanoluciferase assay, the IC50 of CMN was 4.6 μg/mL. Binding of CMN to recombinant Prp8 intein was demonstrated by thermal shift assay and microscale thermophoresis. Treating Cne cells with CMN reduced intein splicing. CMN was fungistatic and showed a synergistic effect with the known antifungal drug amphotericin B. Finally, CMN treatment at 20 mg/kg body weight led to 60% reduction in lung fungal load in a cryptococcal pulmonary infection mouse model. Overall, CMN represents a potent antifungal with a novel mechanism of action to treat Cne and possibly Cga infections.
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Affiliation(s)
- Anil Mathew Tharappel
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Yan Chun Zhu
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Xiangmeng Wu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
| | - Sudha Chaturvedi
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
- The BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
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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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Wall DA, Tarrant SP, Wang C, Mills KV, Lennon CW. Intein Inhibitors as Novel Antimicrobials: Protein Splicing in Human Pathogens, Screening Methods, and Off-Target Considerations. Front Mol Biosci 2021; 8:752824. [PMID: 34692773 PMCID: PMC8529194 DOI: 10.3389/fmolb.2021.752824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 01/20/2023] Open
Abstract
Protein splicing is a post-translational process by which an intervening polypeptide, or intein, catalyzes its own removal from the flanking polypeptides, or exteins, concomitant with extein ligation. Although inteins are highly abundant in the microbial world, including within several human pathogens, they are absent in the genomes of metazoans. As protein splicing is required to permit function of essential proteins within pathogens, inteins represent attractive antimicrobial targets. Here we review key proteins interrupted by inteins in pathogenic mycobacteria and fungi, exciting discoveries that provide proof of concept that intein activity can be inhibited and that this inhibition has an effect on the host organism's fitness, and bioanalytical methods that have been used to screen for intein activity. We also consider potential off-target inhibition of hedgehog signaling, given the similarity in structure and function of inteins and hedgehog autoprocessing domains.
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Affiliation(s)
- Diana A Wall
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Seanan P Tarrant
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States.,Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Christopher W Lennon
- Department of Biological Sciences, Murray State University, Murray, KY, United States
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Panda S, Nanda A, Nasker SS, Sen D, Mehra A, Nayak S. Metal effect on intein splicing: A review. Biochimie 2021; 185:53-67. [PMID: 33727137 DOI: 10.1016/j.biochi.2021.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/08/2023]
Abstract
Inteins are intervening polypeptides that interrupt the functional domains of several important proteins across the three domains of life. Inteins excise themselves from the precursor protein, ligating concomitant extein residues in a process called protein splicing. Post-translational auto-removal of inteins remain critical for the generation of active proteins. The perspective of inteins in science is a robust field of research, however fundamental studies centralized upon splicing regulatory mechanism are imperative for addressing more intricate issues. Controlled engineering of intein splicing has many applications; intein inhibition can facilitate novel drug design, while activation of intein splicing is exploited in protein purification. This paper provides a comprehensive review of the past and recent advances in the splicing regulation via metal-intein interaction. We compare the behavior of different metal ions on diverse intein systems. Though metals such as Zn, Cu, Pt, Cd, Co, Ni exhibit intein inhibitory effect heterogeneously on different inteins, divalent metal ions such as Ca and Mg fail to do so. The observed diversity in the metal-intein interaction arises mostly due to intein polymorphism and variations in atomic structure of metals. A mechanistic understanding of intein regulation by metals in native as well as synthetically engineered intein systems may yield potent intein inhibitors via direct or indirect approach.
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Affiliation(s)
- Sunita Panda
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Ananya Nanda
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Sourya Subhra Nasker
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Debjani Sen
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Ashwaria Mehra
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Sasmita Nayak
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India.
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Abstract
Self-splicing proteins, called inteins, are present in many human pathogens, including the emerging fungal threats Cryptococcus neoformans (Cne) and Cryptococcus gattii (Cga), the causative agents of cryptococcosis. Inhibition of protein splicing in Cryptococcus sp. interferes with activity of the only intein-containing protein, Prp8, an essential intron splicing factor. Here, we screened a small-molecule library to find addititonal, potent inhibitors of the Cne Prp8 intein using a split-GFP splicing assay. This revealed the compound 6G-318S, with IC50 values in the low micromolar range in the split-GFP assay and in a complementary split-luciferase system. A fluoride derivative of the compound 6G-318S displayed improved cytotoxicity in human lung carcinoma cells, although there was a slight reduction in the inhibition of splicing. 6G-318S and its derivative inhibited splicing of the Cne Prp8 intein in vivo in Escherichia coli and in C. neoformans Moreover, the compounds repressed growth of WT C. neoformans and C. gattii In contrast, the inhibitors were less potent at inhibiting growth of the inteinless Candida albicans Drug resistance was observed when the Prp8 intein was overexpressed in C. neoformans, indicating specificity of this molecule toward the target. No off-target activity was observed, such as inhibition of serine/cysteine proteases. The inhibitors bound covalently to the Prp8 intein and binding was reduced when the active-site residue Cys1 was mutated. 6G-318S showed a synergistic effect with amphotericin B and additive to indifferent effects with a few other clinically used antimycotics. Overall, the identification of these small-molecule intein-splicing inhibitors opens up prospects for a new class of antifungals.
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Inteins in Science: Evolution to Application. Microorganisms 2020; 8:microorganisms8122004. [PMID: 33339089 PMCID: PMC7765530 DOI: 10.3390/microorganisms8122004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022] Open
Abstract
Inteins are mobile genetic elements that apply standard enzymatic strategies to excise themselves post-translationally from the precursor protein via protein splicing. Since their discovery in the 1990s, recent advances in intein technology allow for them to be implemented as a modern biotechnological contrivance. Radical improvement in the structure and catalytic framework of cis- and trans-splicing inteins devised the development of engineered inteins that contribute to various efficient downstream techniques. Previous literature indicates that implementation of intein-mediated splicing has been extended to in vivo systems. Besides, the homing endonuclease domain also acts as a versatile biotechnological tool involving genetic manipulation and control of monogenic diseases. This review orients the understanding of inteins by sequentially studying the distribution and evolution pattern of intein, thereby highlighting a role in genetic mobility. Further, we include an in-depth summary of specific applications branching from protein purification using self-cleaving tags to protein modification, post-translational processing and labelling, followed by the development of intein-based biosensors. These engineered inteins offer a disruptive approach towards research avenues like biomaterial construction, metabolic engineering and synthetic biology. Therefore, this linear perspective allows for a more comprehensive understanding of intein function and its diverse applications.
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Li Z, Fu B, Green CM, Liu B, Zhang J, Lang Y, Chaturvedi S, Belfort M, Liao G, Li H. Cisplatin protects mice from challenge of Cryptococcus neoformans by targeting the Prp8 intein. Emerg Microbes Infect 2019; 8:895-908. [PMID: 31223062 PMCID: PMC6598491 DOI: 10.1080/22221751.2019.1625727] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/16/2019] [Indexed: 01/02/2023]
Abstract
The Prp8 intein is one of the most widespread eukaryotic inteins, present in important pathogenic fungi, including Cryptococcus and Aspergillus species. Because the processed Prp8 carries out essential and non-redundant cellular functions, a Prp8 intein inhibitor is a mechanistically novel antifungal agent. In this report, we demonstrated that cisplatin, an FDA-approved cancer drug, significantly arrested growth of Prp8 intein-containing fungi C. neoformans and C. gattii, but only poorly inhibited growth of intein-free Candida species. These results suggest that cisplatin arrests fungal growth through specific inhibition of the Prp8 intein. Cisplatin was also found to significantly inhibit growth of C. neoformans in a mouse model. Our results further showed that cisplatin inhibited Prp8 intein splicing in vitro in a dose-dependent manner by direct binding to the Prp8 intein. Crystal structures of the apo- and cisplatin-bound Prp8 inteins revealed that two degenerate cisplatin molecules bind at the intein active site. Mutation of the splicing-site residues led to loss of cisplatin binding, as well as impairment of intein splicing. Finally, we found that overexpression of the Prp8 intein in cryptococcal species conferred cisplatin resistance. Overall, these results indicate that the Prp8 intein is a novel antifungal target worth further investigation.
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Affiliation(s)
- Zhong Li
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Bin Fu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, People’s Republic of China
| | - Cathleen M. Green
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, USA
| | - Binbin Liu
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Jing Zhang
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Yuekun Lang
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Sudha Chaturvedi
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest University, Chongqing, People’s Republic of China
| | - Hongmin Li
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
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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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13
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Intermolecular domain swapping induces intein-mediated protein alternative splicing. Nat Chem Biol 2013; 9:616-22. [DOI: 10.1038/nchembio.1320] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 07/17/2013] [Indexed: 11/09/2022]
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14
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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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Lin Y, Li M, Song H, Xu L, Meng Q, Liu XQ. Protein trans-splicing of multiple atypical split inteins engineered from natural inteins. PLoS One 2013; 8:e59516. [PMID: 23593141 PMCID: PMC3620165 DOI: 10.1371/journal.pone.0059516] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/15/2013] [Indexed: 11/30/2022] Open
Abstract
Protein trans-splicing by split inteins has many uses in protein production and research. Splicing proteins with synthetic peptides, which employs atypical split inteins, is particularly useful for site-specific protein modifications and labeling, because the synthetic peptide can be made to contain a variety of unnatural amino acids and chemical modifications. For this purpose, atypical split inteins need to be engineered to have a small N-intein or C-intein fragment that can be more easily included in a synthetic peptide that also contains a small extein to be trans-spliced onto target proteins. Here we have successfully engineered multiple atypical split inteins capable of protein trans-splicing, by modifying and testing more than a dozen natural inteins. These included both S1 split inteins having a very small (11–12 aa) N-intein fragment and S11 split inteins having a very small (6 aa) C-intein fragment. Four of the new S1 and S11 split inteins showed high efficiencies (85–100%) of protein trans-splicing both in E. coli cells and in vitro. Under in vitro conditions, they exhibited reaction rate constants ranging from ∼1.7×10−4 s−1 to ∼3.8×10−4 s−1, which are comparable to or higher than those of previously reported atypical split inteins. These findings should facilitate a more general use of trans-splicing between proteins and synthetic peptides, by expanding the availability of different atypical split inteins. They also have implications on understanding the structure-function relationship of atypical split inteins, particularly in terms of intein fragment complementation.
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Affiliation(s)
- Ying Lin
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
| | - Mengmeng Li
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
| | - Huiling Song
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lingling Xu
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
- * E-mail: (QM); (XQL)
| | - Xiang-Qin Liu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail: (QM); (XQL)
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Bokor AA, Kohn LM, Poulter RT, van Kan JA. PRP8 inteins in species of the genus Botrytis and other ascomycetes. Fungal Genet Biol 2012; 49:250-61. [DOI: 10.1016/j.fgb.2012.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/16/2011] [Accepted: 01/11/2012] [Indexed: 12/29/2022]
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17
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Zhang L, Zheng Y, Callahan B, Belfort M, Liu Y. Cisplatin inhibits protein splicing, suggesting inteins as therapeutic targets in mycobacteria. J Biol Chem 2010; 286:1277-82. [PMID: 21059649 DOI: 10.1074/jbc.m110.171124] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis harbors three protein splicing elements, called inteins, in critical genes and their protein products. Post-translational removal of the inteins occurs autocatalytically and is required for function of the respective M. tuberculosis proteins. Inteins are therefore potential targets for antimycobacterial agents. In this work, we report that the splicing activity of the intein present in the RecA recombinase of M. tuberculosis is potently inhibited by the anticancer drug cisplatin (cis-diamminedichloro-platinum(II)). This previously unrecognized activity of cisplatin was established using both an in vitro intein splicing assay, which yielded an IC(50) of ∼2 μM, and a genetic reporter for intein splicing in Escherichia coli. Testing of related platinum(II) complexes indicated that the inhibition activity is highly structure-dependent, with cisplatin exhibiting the best inhibitory effect. Finally, we report that cisplatin is toxic toward M. tuberculosis with a minimum inhibitory concentration of ∼40 μM, and in genetic experiments conducted with the related Mycobacterium bovis bacillus Calmette-Guérrin (BCG) strain, we show that cisplatin toxicity can be mitigated by intein overexpression. We propose that cisplatin inhibits intein activity by modifying at least one conserved cysteine residue that is required for splicing. Together these results identify a novel active site inhibitor of inteins and validate inteins as viable targets for small molecule inhibition in mycobacteria.
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Affiliation(s)
- Liyun Zhang
- Department of Chemistry, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, China
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18
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Theodoro RC, Volkmann G, Liu XQ, Bagagli E. PRP8 intein in Ajellomycetaceae family pathogens: sequence analysis, splicing evaluation and homing endonuclease activity. Fungal Genet Biol 2010; 48:80-91. [PMID: 20682355 DOI: 10.1016/j.fgb.2010.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 04/28/2010] [Accepted: 07/22/2010] [Indexed: 12/25/2022]
Abstract
Inteins are intervening sequences that are transcribed and translated with flanking host protein sequences and then self-excised by protein splicing. Bi-functional inteins also contain a homing endonuclease responsible for their genetic mobility. The PRP8 intein, the most widespread among fungi, occurs in important pathogens such as Histoplasma capsulatum and Paracoccidioides brasiliensis, from the Ajellomycetaceae family. Herein, we describe the bi-functional PRP8 intein in two other Ajellomycetacean pathogens, Blastomyces dermatitidis and Emmonsia parva. Sequence analysis and experimental evidence suggest that the homing endonuclease from PbrPRP8 is inactive. The splicing activity of the PRP8 intein from the B. dermatitidis, E. parva and P. brasiliensis species complex was demonstrated in a non-native protein context in Escherichia coli. Since the PRP8 intein is located in a functionally essential nuclear protein, it can be considered a promising therapeutic target for anti-fungal drugs, because inhibition of intein splicing should inhibit proliferation of intein-containing pathogens.
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Affiliation(s)
- Raquel Cordeiro Theodoro
- Department of Microbiology and Immunology, Institute of Biosciences, UNESP, Botucatu, SP, Brazil
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Sexual mating of Botrytis cinerea illustrates PRP8 intein HEG activity. Fungal Genet Biol 2010; 47:392-8. [PMID: 20093192 DOI: 10.1016/j.fgb.2010.01.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 01/13/2010] [Indexed: 01/15/2023]
Abstract
Strains of Botrytis cinerea are polymorphic for the presence of an intein in the Prp8 gene (intein +/-). The intein encodes a homing endonuclease (HEG). During meiosis in an intein +/- heterozygote, the homing endonuclease initiates intein 'homing' by inducing gene conversion. In such meioses, the homing endonuclease triggers gene conversion of the intein together with its flanking sequences into the empty allele. The efficiency of gene conversion of the intein was found to be 100%. The extent of flanking sequence affected by the gene conversion varied in different meioses. A survey of the inteins and flanking sequences of a group B. cinerea isolates indicates that there are two distinct variants of the intein both of which have active HEGs. The survey also suggests that the intein has been actively homing during the evolution of the species and that the PRP8 intein may have entered the species by horizontal transfer.
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Theodoro RC, Bagagli E. Inteins in pathogenic fungi: a phylogenetic tool and perspectives for therapeutic applications. Mem Inst Oswaldo Cruz 2009; 104:497-504. [PMID: 19547879 DOI: 10.1590/s0074-02762009000300017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 03/13/2009] [Indexed: 01/18/2023] Open
Abstract
Inteins or 'internal proteins' are coding sequences that are transcribed and translated with flanking sequences (exteins). After translation, the inteins are excised by an autocatalytic process and the host protein assumes its normal conformation and develops its expected function. These parasitic genetic elements have been found in important, conserved proteins in all three domains of life. Most of the eukaryotic inteins are present in the fungi kingdom and the PRP8 intein is one of the most widespread inteins, occurring in important pathogens such as Cryptococcus neoformans (varieties grubii and neoformans), Cryptococcus gattii, Histoplasma capsulatum and Paracoccidioides brasiliensis. The knowledge of conserved and non-conserved domains in inteins have opened up new opportunities for the study of population variability in pathogenic fungi, including their phylogenetic relationships and recognition or diagnoses of species. Furthermore, inteins in pathogenic fungi should also be considered a promising therapeutic drug target, since once the autocatalytic splicing is inhibited, the host protein, which is typically vital, will not be able to perform its normal function and the fungal cell will not survive or reproduce.
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Affiliation(s)
- Raquel Cordeiro Theodoro
- Departamento de Microbiologia e Imunologia, Instituto de Biociências, UNESP, Botucatu, São Paulo, Brasil
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Elleuche S, Pelikan C, Nolting N, Pöggeler S. Inteins and introns within the prp8 -gene of four Eupenicillium species. J Basic Microbiol 2009; 49:52-7. [PMID: 19253333 DOI: 10.1002/jobm.200800168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Inteins are protein-intervening sequences that are translated with the host protein and can self-excise themselves post-translationally in an autocatalytic process. The flanking regions--called exteins--are then re-ligated with a new peptide bond, resulting in a mature host protein. Previously, we have identified inteins in the highly conserved 3.2 region of the PRP8 protein from species of the genus Penicillium. These inteins are integrated at the same position as that which has recently been described in PRP8 proteins from different strains of Cryptococcus neoformans and several ascomycetes. In this study, we investigated the presence of PRP8 inteins in four members of the genus Eupenicillium. Two species of this genus, Eupenicillium crustaceum and Eupenicillium baarnense, contain an intein at the same insertion site. Both inteins are mini-inteins and undergo self-splicing when heterologously expressed with a model host protein in Escherichia coli. Interestingly, we identified introns in the prp8-sequence encoding the 3.2 regions of the PRP8 protein in Eupenicillium meridianum and Eupenicillium terrenum. The introns are located 13 bps and 15 bps downstream of the putative intein insertion site. Here, we consider that the lack of inteins in these two species might be due to the prevention of endonuclease-mediated intein propagation in the intron-containing prp8-sequences.
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Affiliation(s)
- Skander Elleuche
- Georg-August Universität Göttingen, Institut für Mikrobiologie und Genetik, Abteilung für Genetik eukaryotischer Mikroorganismen, 37077 Göttingen, Germany
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Appleby JH, Zhou K, Volkmann G, Liu XQ. Novel Split Intein for trans-Splicing Synthetic Peptide onto C Terminus of Protein. J Biol Chem 2009; 284:6194-9. [DOI: 10.1074/jbc.m805474200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Theodoro RC, Bagagli E, Oliveira C. Phylogenetic analysis of PRP8 intein in Paracoccidioides brasiliensis species complex. Fungal Genet Biol 2008; 45:1284-91. [DOI: 10.1016/j.fgb.2008.07.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 06/24/2008] [Accepted: 07/06/2008] [Indexed: 01/24/2023]
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24
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Minimization of a eukaryotic mini-intein. Biochem Biophys Res Commun 2008; 366:239-43. [DOI: 10.1016/j.bbrc.2007.11.126] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Accepted: 11/23/2007] [Indexed: 02/06/2023]
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Pearl EJ, Bokor AAM, Butler MI, Poulter RTM, Wilbanks SM. Preceding hydrophobic and beta-branched amino acids attenuate splicing by the CnePRP8 intein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:995-1001. [PMID: 17604706 DOI: 10.1016/j.bbapap.2007.05.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 05/23/2007] [Accepted: 05/29/2007] [Indexed: 11/18/2022]
Abstract
As the Cne PRP8 intein is active and exists in an essential gene of an important fungal pathogen, inhibitors of splicing and assays for intein activity are of interest. The self-splicing activity of Cne PRP8, the intein from the Prp8 gene of Cryptococcus neoformans, was assessed in different heterologous fusion proteins expressed in Escherichia coli. Placement of a putatively inactive variant of the intein adjacent to the alpha-complementation peptide abolished the peptide's ability to restore beta-galactosidase activity, while an active variant allowed complementation. This alpha-complementation peptide therefore provides a facile assay of splicing which can be used to test potential inhibitors. When placed between two heterologous protein domains, splicing was impaired by a beta-branched amino acid immediately preceding the intein, while splicing occurred only with a hydroxyl or thiol immediately following the intein. Both these assays sensitively report impairment of splicing and provide information on how context constrains the splicing ability of Cne PRP8.
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Affiliation(s)
- Esther J Pearl
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
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Elleuche S, Pöggeler S. Trans-splicing of an artificially split fungal mini-intein. Biochem Biophys Res Commun 2007; 355:830-4. [PMID: 17316565 DOI: 10.1016/j.bbrc.2007.02.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 02/08/2007] [Indexed: 10/23/2022]
Abstract
Inteins are internal protein domains found inside the coding region of different proteins. They can autocatalytically self-excise from their host protein and ligate the protein flanks, called exteins, with a peptide bond via a post-translational process called protein cis-splicing. In contrast, protein trans-splicing involves inteins split into an N- and a C-terminal domain. Both domains are synthesized as two separate components and each joined to an extein; the intein domains can reassemble and link the joined exteins into one functional protein. In this study, we introduced three split sites into the PRP8 mini-intein of Penicillium chrysogenum and demonstrated for the first time trans-splicing of a fungal PRP8 intein. Two of the sites introduced allowed splicing to occur in trans while the third was not functional.
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Affiliation(s)
- Skander Elleuche
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August-University of Göttingen, Germany
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Goodwin TJD, Butler MI, Poulter RTM. Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes. BMC Biol 2006; 4:38. [PMID: 17069655 PMCID: PMC1635734 DOI: 10.1186/1741-7007-4-38] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 10/27/2006] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Inteins are self-splicing protein elements. They are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins) with a peptide bond. They are encoded as in-frame insertions within the genes for the host proteins. Inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. Only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these are from ascomycete or basidiomycete fungi. RESULTS We identified seven intein coding sequences within nuclear genes coding for the second largest subunits of RNA polymerase. These sequences were found in diverse eukaryotes: one is in the second largest subunit of RNA polymerase I (RPA2) from the ascomycete fungus Phaeosphaeria nodorum, one is in the RNA polymerase III (RPC2) of the slime mould Dictyostelium discoideum and four intein coding sequences are in RNA polymerase II genes (RPB2), one each from the green alga Chlamydomonas reinhardtii, the zygomycete fungus Spiromyces aspiralis and the chytrid fungi Batrachochytrium dendrobatidis and Coelomomyces stegomyiae. The remaining intein coding sequence is in a viral relic embedded within the genome of the oomycete Phytophthora ramorum. The Chlamydomonas and Dictyostelium inteins are the first nuclear-encoded inteins found outside of the fungi. These new inteins represent a unique dataset: they are found in homologous proteins that form a paralogous group. Although these paralogues diverged early in eukaryotic evolution, their sequences can be aligned over most of their length. The inteins are inserted at multiple distinct sites, each of which corresponds to a highly conserved region of RNA polymerase. This dataset supports earlier work suggesting that inteins preferentially occur in highly conserved regions of their host proteins. CONCLUSION The identification of these new inteins increases the known host range of intein sequences in eukaryotes, and provides fresh insights into their origins and evolution. We conclude that inteins are ancient eukaryote elements once found widely among microbial eukaryotes. They persist as rarities in the genomes of a sporadic array of microorganisms, occupying highly conserved sites in diverse proteins.
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Affiliation(s)
- Timothy JD Goodwin
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Margaret I Butler
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Russell TM Poulter
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
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Butler MI, Gray J, Goodwin TJD, Poulter RTM. The distribution and evolutionary history of the PRP8 intein. BMC Evol Biol 2006; 6:42. [PMID: 16737526 PMCID: PMC1508164 DOI: 10.1186/1471-2148-6-42] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Accepted: 05/31/2006] [Indexed: 12/31/2022] Open
Abstract
Background We recently described a mini-intein in the PRP8 gene of a strain of the basidiomycete Cryptococcus neoformans, an important fungal pathogen of humans. This was the second described intein in the nuclear genome of any eukaryote; the first nuclear encoded intein was found in the VMA gene of several saccharomycete yeasts. The evolution of eukaryote inteins is not well understood. In this report we describe additional PRP8 inteins (bringing the total of these to over 20). We compare and contrast the phylogenetic distribution and evolutionary history of the PRP8 intein and the saccharomycete VMA intein, in order to derive a broader understanding of eukaryote intein evolution. It has been suggested that eukaryote inteins undergo horizontal transfer and the present analysis explores this proposal. Results In total, 22 PRP8 inteins have been detected in species from three different orders of euascomycetes, including Aspergillus nidulans and Aspergillus fumigatus (Eurotiales), Paracoccidiodes brasiliensis, Uncinocarpus reesii and Histoplasma capsulatum (Onygales) and Botrytis cinerea (Helotiales). These inteins are all at the same site in the PRP8 sequence as the original Cryptococcus neoformans intein. Some of the PRP8 inteins contain apparently intact homing endonuclease domains and are thus potentially mobile, while some lack the region corresponding to the homing endonuclease and are thus mini-inteins. In contrast, no mini-inteins have been reported in the VMA gene of yeast. There are several examples of pairs of closely related species where one species carries the PRP8 intein while the intein is absent from the other species. Bio-informatic and phylogenetic analyses suggest that many of the ascomycete PRP8 homing endonucleases are active. This contrasts with the VMA homing endonucleases, most of which are inactive. Conclusion PRP8 inteins are widespread in the euascomycetes (Pezizomycota) and apparently their homing endonucleases are active. There is no evidence for horizontal transfer within the euascomycetes. This suggests that the intein is of ancient origin and has been vertically transmitted amongst the euascomycetes. It is possible that horizontal transfer has occurred between the euascomycetes and members of the basidiomycete genus Cryptococcus.
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Affiliation(s)
- Margaret I Butler
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Jeremy Gray
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Timothy JD Goodwin
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Russell TM Poulter
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
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Elleuche S, Nolting N, Pöggeler S. Protein splicing of PRP8 mini-inteins from species of the genus Penicillium. Appl Microbiol Biotechnol 2006; 72:959-67. [PMID: 16544141 DOI: 10.1007/s00253-006-0350-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 01/20/2006] [Accepted: 01/23/2006] [Indexed: 11/26/2022]
Abstract
Inteins are protein-intervening sequences found inside the coding region of different host proteins and are translated in-frame with them. They can self-excise through protein splicing, which ligates the host protein flanks with a peptide bond. In this study, four different species of the genus Penicillium were investigated for the presence of inteins inside the conserved splicing-factor protein PRP8. We identified 157 to 162 amino acid in-frame insertions in the PRP8 protein of Penicillium chrysogenum, Penicillium expansum, and Penicillium vulpinum (formerly Penicillium claviforme). The Penicillium PRP8 inteins are mini-inteins without a conserved endonuclease domain. We demonstrated that the PRP8 mini-inteins of P. chrysogenum, P. expansum, and P. vulpinum undergo autocatalytic protein splicing when heterologously expressed in E. coli, in a model host protein, and in a divided GFP model system. They are, thus, among the smallest known nuclear-encoded, active splicing protein elements. The GFP assay should be valuable as a screening system for protein splicing inhibitors as potential antimycotic agents and as tools for studying the mechanism of protein splicing of fungal mini-inteins.
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Affiliation(s)
- Skander Elleuche
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Bochum, Germany
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Abstract
Comparative analyses of fungal genomes and molecular research on genes associated with fungal viability and virulence has led to the identification of many putative targets for novel antifungal agents. So far the rational approach to antifungal discovery, in which compounds are optimized against an individual target then progressed to efficacy against intact fungi and ultimately to infected humans has delivered no new agents. However, the approach continues to hold promise for the future. This review critically assesses the molecular target-based approach to antifungal discovery, outlines problems and pitfalls inherent in the genomics and target discovery strategies and describes the status of heavily investigated examples of target-based research.
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Affiliation(s)
- Frank C Odds
- Aberdeen Fungal Group, Institute of Medical Sciences, Department of Molecular and Cell Biology, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
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Abstract
Until recently the only intein known to be encoded by the nuclear genome of a eukaryote was the VMA intein in the vacuolar ATPase precursor of several species of saccharomycete yeast. This intein has been intensively studied and much information has been gained about its structure, mode of action and evolutionary history. We recently reported a second nuclear intein, Cne PRP8, encoded within the PRP8 gene of the basidiomycete Cryptococcus neoformans. Subsequent studies have found allelic PRP8 inteins in several species of yeast and filamentous ascomycetes. Here we report two further, non-allelic, inteins from ascomycete species. The yeast Debaryomyces hansenii (which also has a VMA intein) has an intein encoded within the sequence of the glutamate synthase gene (GLT1). There are also inteins encoded in the homologous GLT1 genes of the yeast Candida (Pichia) guilliermondii and the filamentous fungus Podospora anserina. These allelic GLT1 inteins occupy exactly the same site in the glutamate synthase and all contain domains that indicate the presence of a homing endonuclease (HEG). Podospora anserina, in addition, contains a second, non-allelic, intein encoded in the chitin synthase gene (CHS2); this intein also contains a HEG domain. We describe the phylogenetic relationships among the four eukaryote nuclear encoded inteins (VMA, PRP8, GLT1 and CHS2). We also consider this phylogeny in the broader context of eubacterial, archaeal and eukaryote viral and organelle inteins.
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Affiliation(s)
- Margaret I Butler
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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Rementeria A, López-Molina N, Ludwig A, Vivanco AB, Bikandi J, Pontón J, Garaizar J. Genes and molecules involved in Aspergillus fumigatus virulence. Rev Iberoam Micol 2005; 22:1-23. [PMID: 15813678 DOI: 10.1016/s1130-1406(05)70001-2] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Aspergillus fumigatus causes a wide range of diseases that include mycotoxicosis, allergic reactions and systemic diseases (invasive aspergillosis) with high mortality rates. Pathogenicity depends on immune status of patients and fungal strain. There is no unique essential virulence factor for development of this fungus in the patient and its virulence appears to be under polygenetic control. The group of molecules and genes associated with the virulence of this fungus includes many cell wall components, such as beta-(1-3)-glucan, galactomannan, galactomannanproteins (Afmp1 and Afmp2), and the chitin synthetases (Chs; chsE and chsG), as well as others. Some genes and molecules have been implicated in evasion from the immune response, such as the rodlets layer (rodA/hyp1 gene) and the conidial melanin-DHN (pksP/alb1 gene). The detoxifying systems for Reactive Oxygen Species (ROS) by catalases (Cat1p and Cat2p) and superoxide dismutases (MnSOD and Cu, ZnSOD), had also been pointed out as essential for virulence. In addition, this fungus produces toxins (14 kDa diffusible substance from conidia, fumigaclavin C, aurasperon C, gliotoxin, helvolic acid, fumagilin, Asp-hemolysin, and ribotoxin Asp fI/mitogilin F/restrictocin), allergens (Asp f1 to Asp f23), and enzymatic proteins as alkaline serin proteases (Alp and Alp2), metalloproteases (Mep), aspartic proteases (Pep and Pep2), dipeptidyl-peptidases (DppIV and DppV), phospholipase C and phospholipase B (Plb1 and Plb2). These toxic substances and enzymes seems to be additive and/or synergistic, decreasing the survival rates of the infected animals due to their direct action on cells or supporting microbial invasion during infection. Adaptation ability to different trophic situations is an essential attribute of most pathogens. To maintain its virulence attributes A. fumigatus requires iron obtaining by hydroxamate type siderophores (ornitin monooxigenase/SidA), phosphorous obtaining (fos1, fos2, and fos3), signal transductional falls that regulate morphogenesis and/or usage of nutrients as nitrogen (rasA, rasB, rhbA), mitogen activated kinases (sakA codified MAP-kinase), AMPc-Pka signal transductional route, as well as others. In addition, they seem to be essential in this field the amino acid biosynthesis (cpcA and homoaconitase/lysF), the activation and expression of some genes at 37 degrees C (Hsp1/Asp f12, cgrA), some molecules and genes that maintain cellular viability (smcA, Prp8, anexins), etc. Conversely, knowledge about relationship between pathogen and immune response of the host has been improved, opening new research possibilities. The involvement of non-professional cells (endothelial, and tracheal and alveolar epithelial cells) and professional cells (natural killer or NK, and dendritic cells) in infection has been also observed. Pathogen Associated Molecular Patterns (PAMP) and Patterns Recognizing Receptors (PRR; as Toll like receptors TLR-2 and TLR-4) could influence inflammatory response and dominant cytokine profile, and consequently Th response to infec tion. Superficial components of fungus and host cell surface receptors driving these phenomena are still unknown, although some molecules already associated with its virulence could also be involved. Sequencing of A. fumigatus genome and study of gene expression during their infective process by using DNA microarray and biochips, promises to improve the knowledge of virulence of this fungus.
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Affiliation(s)
- Aitor Rementeria
- Departamento Inmunología, Microbiología y Parasitología, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Spain.
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Abstract
Pre-messenger RNA (pre-mRNA) splicing is a central step in gene expression. Lying between transcription and protein synthesis, pre-mRNA splicing removes sequences (introns) that would otherwise disrupt the coding potential of intron-containing transcripts. This process takes place in the nucleus, catalyzed by a large RNA-protein complex called the spliceosome. Prp8p, one of the largest and most highly conserved of nuclear proteins, occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there. Recently, Prp8p has also come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa.Prp8 is unique, having no obvious homology to other proteins; however, using bioinformatical analysis we reveal the presence of a conserved RNA recognition motif (RRM), an MPN/JAB domain and a putative nuclear localization signal (NLS). Here, we review biochemical and genetical data, mostly related to the human and yeast proteins, that describe Prp8's central role within the spliceosome and its molecular interactions during spliceosome formation, as splicing proceeds, and in post-splicing complexes.
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Affiliation(s)
- Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
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Butler MI, Poulter RTM. The PRP8 inteins in Cryptococcus are a source of phylogenetic and epidemiological information. Fungal Genet Biol 2005; 42:452-63. [PMID: 15809009 DOI: 10.1016/j.fgb.2005.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 01/20/2005] [Accepted: 01/25/2005] [Indexed: 11/17/2022]
Abstract
Only two nuclear encoded inteins have been described. The first, SceVMA, was found in a vacuolar ATPase gene of Saccharomyces cerevisiae and related yeasts. The second, CnePRP8, was found in the PRP8 gene of Cryptococcus neoformans. CnePRP8 contains protein sequences associated with intein splicing but no endonuclease domain. We compared allelic mini-inteins in both varieties of C. neoformans (var. neoformans and var. grubii) and in the related primary pathogen C. gattii to study the evolution of both the mini-intein and the host. We also describe a full-length, endonuclease-containing intein in Cryptococcus laurentii, a moderately distant relation of C. neoformans. We did not detect an intein in the PRP8 gene of other species of Cryptococcus including species closely related to the C. neoformans/C. gattii group. It is therefore probable that the C. neoformans/C. gattii mini-intein was derived from horizontal transfer in which C. laurentii or another intein-containing species was the source.
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Affiliation(s)
- Margaret I Butler
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand.
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