1
|
Osborne M, Fubara A, Ó Cinnéide E, Coughlan AY, Wolfe KH. WHO elements - A new category of selfish genetic elements at the borderline between homing elements and transposable elements. Semin Cell Dev Biol 2024; 163:2-13. [PMID: 38664119 DOI: 10.1016/j.semcdb.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene FBA1. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (FBA1), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the FBA1 locus, the result of an 'arms race' between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the FBA1 locus and instead appears to have become transposable, inserting at random genomic sites in Torulaspora globosa with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.
Collapse
Affiliation(s)
- Matthieu Osborne
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Athaliah Fubara
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Eoin Ó Cinnéide
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Aisling Y Coughlan
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
| |
Collapse
|
2
|
Anastassov S, Filo M, Khammash M. Inteins: A Swiss army knife for synthetic biology. Biotechnol Adv 2024; 73:108349. [PMID: 38552727 DOI: 10.1016/j.biotechadv.2024.108349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/13/2024]
Abstract
Inteins are proteins found in nature that execute protein splicing. Among them, split inteins stand out for their versatility and adaptability, presenting creative solutions for addressing intricate challenges in various biological applications. Their exquisite attributes, including compactness, reliability, orthogonality, low toxicity, and irreversibility, make them of interest to various fields including synthetic biology, biotechnology and biomedicine. In this review, we delve into the inherent challenges of using inteins, present approaches for overcoming these challenges, and detail their reliable use for specific cellular tasks. We will discuss the use of conditional inteins in areas like cancer therapy, drug screening, patterning, infection treatment, diagnostics and biocontainment. Additionally, we will underscore the potential of inteins in executing basic logical operations with practical implications. We conclude by showcasing their potential in crafting complex genetic circuits for performing computations and feedback control that achieves robust perfect adaptation.
Collapse
Affiliation(s)
- Stanislav Anastassov
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland
| | - Maurice Filo
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland.
| |
Collapse
|
3
|
Gastineau R, Lemieux C, Turmel M, Otis C, Boyle B, Coulis M, Gouraud C, Boag B, Murchie AK, Winsor L, Justine JL. The invasive land flatworm Arthurdendyus triangulatus has repeated sequences in the mitogenome, extra-long cox2 gene and paralogous nuclear rRNA clusters. Sci Rep 2024; 14:7840. [PMID: 38570596 PMCID: PMC10991399 DOI: 10.1038/s41598-024-58600-y] [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] [Received: 12/21/2023] [Accepted: 04/01/2024] [Indexed: 04/05/2024] Open
Abstract
Using a combination of short- and long-reads sequencing, we were able to sequence the complete mitochondrial genome of the invasive 'New Zealand flatworm' Arthurdendyus triangulatus (Geoplanidae, Rhynchodeminae, Caenoplanini) and its two complete paralogous nuclear rRNA gene clusters. The mitogenome has a total length of 20,309 bp and contains repetitions that includes two types of tandem-repeats that could not be solved by short-reads sequencing. We also sequenced for the first time the mitogenomes of four species of Caenoplana (Caenoplanini). A maximum likelihood phylogeny associated A. triangulatus with the other Caenoplanini but Parakontikia ventrolineata and Australopacifica atrata were rejected from the Caenoplanini and associated instead with the Rhynchodemini, with Platydemus manokwari. It was found that the mitogenomes of all species of the subfamily Rhynchodeminae share several unusual structural features, including a very long cox2 gene. This is the first time that the complete paralogous rRNA clusters, which differ in length, sequence and seemingly number of copies, were obtained for a Geoplanidae.
Collapse
Affiliation(s)
- Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland.
| | - Claude Lemieux
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Monique Turmel
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Christian Otis
- Plateforme d'Analyse Génomique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Brian Boyle
- Plateforme d'Analyse Génomique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Mathieu Coulis
- CIRAD, UPR GECO, 97285, Le Lamentin, Martinique, France
- GECO, CIRAD, University Montpellier, Montpellier, France
| | - Clément Gouraud
- UMR CNRS 6553 Ecobio, Université de Rennes, 263 Avenue du Gal Leclerc, CS 74205, CEDEX, 35042, Rennes, France
| | - Brian Boag
- The James Hutton Institute, Invergowrie, DD2 5DA, Scotland
| | - Archie K Murchie
- Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, BT9 5PX, Northern Ireland
| | - Leigh Winsor
- College of Science and Engineering, James Cook University of North Queensland, Townsville, QLD, Australia
| | - Jean-Lou Justine
- ISYEB, Institut de Systématique, Évolution, Biodiversité (UMR7205 CNRS, EPHE, MNHN, UPMC, Université des Antilles), Muséum National d'Histoire Naturelle, CP 51, 55 Rue Buffon, 75231, Paris Cedex 05, France
| |
Collapse
|
4
|
Benson CW, Sheltra MR, Huff DR. The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss. G3 (BETHESDA, MD.) 2024; 14:jkad238. [PMID: 37847611 PMCID: PMC10849329 DOI: 10.1093/g3journal/jkad238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
To complete its parasitic lifecycle, Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloëana's ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloëana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloëana is nested within the genus Tilletia and diverged from Tilletia caries and Tilletia walkeri ∼40 MYA. We find that S. buchloëana contains a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes, and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloëana's evolution and host specificity. Salmacisia buchloëana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation, and that S. buchloëana has a unique bias for the serine codon UCG. Finally, we identify 3 inteins within the S. buchloëana genome, 2 of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.
Collapse
Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
| |
Collapse
|
5
|
Gallot-Lavallée L, Jerlström-Hultqvist J, Zegarra-Vidarte P, Salas-Leiva DE, Stairs CW, Čepička I, Roger AJ, Archibald JM. Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes. Proc Natl Acad Sci U S A 2023; 120:e2306381120. [PMID: 38019867 PMCID: PMC10710043 DOI: 10.1073/pnas.2306381120] [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] [Received: 04/19/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Inteins are self-splicing protein elements found in viruses and all three domains of life. How the DNA encoding these selfish elements spreads within and between genomes is poorly understood, particularly in eukaryotes where inteins are scarce. Here, we show that the nuclear genomes of three strains of Anaeramoeba encode between 45 and 103 inteins, in stark contrast to four found in the most intein-rich eukaryotic genome described previously. The Anaeramoeba inteins reside in a wide range of proteins, only some of which correspond to intein-containing proteins in other eukaryotes, prokaryotes, and viruses. Our data also suggest that viruses have contributed to the spread of inteins in Anaeramoeba and the colonization of new alleles. The persistence of Anaeramoeba inteins might be partly explained by intragenomic movement of intein-encoding regions from gene to gene. Our intein dataset greatly expands the spectrum of intein-containing proteins and provides insights into the evolution of inteins in eukaryotes.
Collapse
Affiliation(s)
- Lucie Gallot-Lavallée
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
| | - Jon Jerlström-Hultqvist
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala751 24, Sweden
| | - Paula Zegarra-Vidarte
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala751 24, Sweden
| | - Dayana E. Salas-Leiva
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
| | - Courtney W. Stairs
- Microbiology Group, Department of Biology, Lund University, Lund223 62, Sweden
| | - Ivan Čepička
- Department of Zoology, Charles University, Prague128 00, Czech Republic
| | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova ScotiaB3H 4R2, Canada
| |
Collapse
|
6
|
Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
Collapse
Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
7
|
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.
Collapse
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.)
| |
Collapse
|
8
|
Mating-Type Switching in Budding Yeasts, from Flip/Flop Inversion to Cassette Mechanisms. Microbiol Mol Biol Rev 2022; 86:e0000721. [PMID: 35195440 PMCID: PMC8941940 DOI: 10.1128/mmbr.00007-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mating-type switching is a natural but unusual genetic control process that regulates cell identity in ascomycete yeasts. It involves physically replacing one small piece of genomic DNA by another, resulting in replacement of the master regulatory genes in the mating pathway and hence a switch of cell type and mating behavior. In this review, we concentrate on recent progress that has been made on understanding the origins and evolution of mating-type switching systems in budding yeasts (subphylum Saccharomycotina). Because of the unusual nature and the complexity of the mechanism in Saccharomyces cerevisiae, mating-type switching was assumed until recently to have originated only once or twice during yeast evolution. However, comparative genomics analysis now shows that switching mechanisms arose many times independently-at least 11 times in budding yeasts and once in fission yeasts-a dramatic example of convergent evolution. Most of these lineages switch mating types by a flip/flop mechanism that inverts a section of a chromosome and is simpler than the well-characterized 3-locus cassette mechanism (MAT/HML/HMR) used by S. cerevisiae. Mating-type switching (secondary homothallism) is one of the two possible mechanisms by which a yeast species can become self-fertile. The other mechanism (primary homothallism) has also emerged independently in multiple evolutionary lineages of budding yeasts, indicating that homothallism has been favored strongly by natural selection. Recent work shows that HO endonuclease, which makes the double-strand DNA break that initiates switching at the S. cerevisiae MAT locus, evolved from an unusual mobile genetic element that originally targeted a glycolytic gene, FBA1.
Collapse
|
9
|
Beyer HM, Iwaï H. Structural Basis for the Propagation of Homing Endonuclease-Associated Inteins. Front Mol Biosci 2022; 9:855511. [PMID: 35372505 PMCID: PMC8966425 DOI: 10.3389/fmolb.2022.855511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Inteins catalyze their removal from a host protein through protein splicing. Inteins that contain an additional site-specific endonuclease domain display genetic mobility via a process termed “homing” and thereby act as selfish DNA elements. We elucidated the crystal structures of two archaeal inteins associated with an active or inactive homing endonuclease domain. This analysis illustrated structural diversity in the accessory domains (ACDs) associated with the homing endonuclease domain. To augment homing endonucleases with highly specific DNA cleaving activity using the intein scaffold, we engineered the ACDs and characterized their homing site recognition. Protein engineering of the ACDs in the inteins illuminated a possible strategy for how inteins could avoid their extinction but spread via the acquisition of a diverse accessory domain.
Collapse
Affiliation(s)
- Hannes M. Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- *Correspondence: Hideo Iwaï, or,
| |
Collapse
|
10
|
Orłowska M, Muszewska A. In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi. J Fungi (Basel) 2022; 8:67. [PMID: 35050007 PMCID: PMC8778642 DOI: 10.3390/jof8010067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/16/2022] Open
Abstract
Early-diverging fungi (EDF) are ubiquitous and versatile. Their diversity is reflected in their genome sizes and complexity. For instance, multiple protein families have been reported to expand or disappear either in particular genomes or even whole lineages. The most commonly mentioned are CAZymes (carbohydrate-active enzymes), peptidases and transporters that serve multiple biological roles connected to, e.g., metabolism and nutrients intake. In order to study the link between ecology and its genomic underpinnings in a more comprehensive manner, we carried out a systematic in silico survey of protein family expansions and losses among EDF with diverse lifestyles. We found that 86 protein families are represented differently according to EDF ecological features (assessed by median count differences). Among these there are 19 families of proteases, 43 CAZymes and 24 transporters. Some of these protein families have been recognized before as serine and metallopeptidases, cellulases and other nutrition-related enzymes. Other clearly pronounced differences refer to cell wall remodelling and glycosylation. We hypothesize that these protein families altogether define the preliminary fungal adaptasome. However, our findings need experimental validation. Many of the protein families have never been characterized in fungi and are discussed in the light of fungal ecology for the first time.
Collapse
Affiliation(s)
- Małgorzata Orłowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| |
Collapse
|
11
|
Mini-Intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins. Microorganisms 2021; 9:microorganisms9061226. [PMID: 34198729 PMCID: PMC8229266 DOI: 10.3390/microorganisms9061226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/26/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022] Open
Abstract
Inteins are prevalent among extremophiles. Mini-inteins with robust splicing properties are of particular interest for biotechnological applications due to their small size. However, biochemical and structural characterization has still been limited to a small number of inteins, and only a few serve as widely used tools in protein engineering. We determined the crystal structure of a naturally occurring Pol-II mini-intein from Pyrococcus horikoshii and compared all three mini-inteins found in the genome of P. horikoshii. Despite their similar sizes, the comparison revealed distinct differences in the insertions and deletions, implying specific evolutionary pathways from distinct ancestral origins. Our studies suggest that sporadically distributed mini-inteins might be more promising for further protein engineering applications than highly conserved mini-inteins. Structural investigations of additional inteins could guide the shortest path to finding novel robust mini-inteins suitable for various protein engineering purposes.
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
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.
Collapse
|
14
|
Coughlan AY, Lombardi L, Braun-Galleani S, Martos AA, Galeote V, Bigey F, Dequin S, Byrne KP, Wolfe KH. The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family. eLife 2020; 9:55336. [PMID: 32338594 PMCID: PMC7282813 DOI: 10.7554/elife.55336] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/24/2020] [Indexed: 01/07/2023] Open
Abstract
The mating-type switching endonuclease HO plays a central role in the natural life cycle of Saccharomyces cerevisiae, but its evolutionary origin is unknown. HO is a recent addition to yeast genomes, present in only a few genera close to Saccharomyces. Here we show that HO is structurally and phylogenetically related to a family of unorthodox homing genetic elements found in Torulaspora and Lachancea yeasts. These WHO elements home into the aldolase gene FBA1, replacing its 3' end each time they integrate. They resemble inteins but they operate by a different mechanism that does not require protein splicing. We show that a WHO protein cleaves Torulaspora delbrueckii FBA1 efficiently and in an allele-specific manner, leading to DNA repair by gene conversion or NHEJ. The DNA rearrangement steps during WHO element homing are very similar to those during mating-type switching, and indicate that HO is a domesticated WHO-like element. In the same way as a sperm from a male and an egg from a female join together to form an embryo in most animals, yeast cells have two sexes that coordinate how they reproduce. These are called “mating types” and, rather than male or female, an individual yeast cell can either be mating type “a” or “alpha”. Every yeast cell contains the genes for both mating types, and each cell’s mating type is determined by which of those genes it has active. Only one mating type gene can be ‘on’ at a time, but some yeast species can swap mating type on demand by switching the corresponding genes ‘on’ or ‘off’. This switch is unusual. Rather than simply activate one of the genes it already has, the yeast cell keeps an inactive version of each mating type gene tucked away, makes a copy of the gene it wants to be active and pastes that copy into a different location in its genome. To do all of this yeast need another gene called HO. This gene codes for an enzyme that cuts the DNA at the location of the active mating type gene. This makes an opening that allows the cell to replace the ‘a’ gene with the ‘alpha’ gene, or vice versa. This system allows yeast cells to continue mating even if all the cells in a colony start off as the same mating type. But, cutting into the DNA is risky, and can damage the health of the cell. So, why did yeast cells evolve a system that could cause them harm? To find out where the HO gene came from, Coughlan et al. searched through all the available genomes from yeast species for other genes with similar sequences and identified a cluster which they nicknamed “weird HO” genes, or WHO genes for short. Testing these genes revealed that they also code for enzymes that make cuts in the yeast genome, but the way the cell repairs the cuts is different. The WHO genes are jumping genes. When the enzyme encoded by a WHO gene makes a cut in the genome, the yeast cell copies the gene into the gap, allowing the gene to ‘jump’ from one part of the genome to another. It is possible that this was the starting point for the evolution of the HO gene. Changes to a WHO gene could have allowed it to cut into the mating type region of the yeast genome, giving the yeast an opportunity to ‘domesticate’ it. Over time, the yeast cell stopped the WHO gene from jumping into the gap and started using the cut to change its mating type. Understanding how cells adapt genes for different purposes is a key question in evolutionary biology. There are many other examples of domesticated jumping genes in other organisms, including in the human immune system. Understanding the evolution of HO not only sheds light on how yeast mating type switching evolved, but on how other species might harness and adapt their genes.
Collapse
Affiliation(s)
- Aisling Y Coughlan
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Lisa Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | | | - Alexandre Ar Martos
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Virginie Galeote
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Frédéric Bigey
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Sylvie Dequin
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Kevin P Byrne
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H Wolfe
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| |
Collapse
|
15
|
Green CM, Li Z, Smith AD, Novikova O, Bacot-Davis VR, Gao F, Hu S, Banavali NK, Thiele DJ, Li H, Belfort M. Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing. PLoS Biol 2019; 17:e3000104. [PMID: 31600193 PMCID: PMC6805012 DOI: 10.1371/journal.pbio.3000104] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 10/22/2019] [Accepted: 09/13/2019] [Indexed: 01/07/2023] Open
Abstract
The spliceosome is a large ribonucleoprotein complex that removes introns from pre-mRNAs. At its functional core lies the essential pre-mRNA processing factor 8 (Prp8) protein. Across diverse eukaryotes, this protein cofactor of RNA catalysis harbors a self-splicing element called an intein. Inteins in Prp8 are extremely pervasive and are found at 7 different sites in various species. Here, we focus on the Prp8 intein from Cryptococcus neoformans (Cne), a human fungal pathogen. We solved the crystal structure of this intein, revealing structural homology among protein splicing sequences in eukaryotes, including the Hedgehog C terminus. Working with the Cne Prp8 intein in a reporter assay, we find that the biologically relevant divalent metals copper and zinc inhibit intein splicing, albeit by 2 different mechanisms. Copper likely stimulates reversible modifications on a catalytically important cysteine, whereas zinc binds at the terminal asparagine and the same critical cysteine. Importantly, we also show that copper treatment inhibits Prp8 protein splicing in Cne. Lastly, an intein-containing Prp8 precursor model is presented, suggesting that metal-induced protein splicing inhibition would disturb function of both Prp8 and the spliceosome. These results indicate that Prp8 protein splicing can be modulated, with potential functional implications for the spliceosome.
Collapse
Affiliation(s)
- Cathleen M. Green
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Zhong Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Aaron D. Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Valjean R. Bacot-Davis
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Fengshan Gao
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Saiyang Hu
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Nilesh K. Banavali
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
| | - Dennis J. Thiele
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America,Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hongmin Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America,* E-mail: (MB); (HL)
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America,* E-mail: (MB); (HL)
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Kelley DS, Lennon CW, Li Z, Miller MR, Banavali NK, Li H, Belfort M. Mycobacterial DnaB helicase intein as oxidative stress sensor. Nat Commun 2018; 9:4363. [PMID: 30341292 PMCID: PMC6195587 DOI: 10.1038/s41467-018-06554-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/10/2018] [Indexed: 11/09/2022] Open
Abstract
Inteins are widespread self-splicing protein elements emerging as potential post-translational environmental sensors. Here, we describe two inteins within one protein, the Mycobacterium smegmatis replicative helicase DnaB. These inteins, DnaBi1 and DnaBi2, have homology to inteins in pathogens, splice with vastly varied rates, and are differentially responsive to environmental stressors. Whereas DnaBi1 splicing is reversibly inhibited by oxidative and nitrosative insults, DnaBi2 is not. Using a reporter that measures splicing in a native intein-containing organism and western blotting, we show that H2O2 inhibits DnaBi1 splicing in M. smegmatis. Intriguingly, upon oxidation, the catalytic cysteine of DnaBi1 forms an intramolecular disulfide bond. We report a crystal structure of the class 3 DnaBi1 intein at 1.95 Å, supporting our findings and providing insight into this splicing mechanism. We propose that this cysteine toggle allows DnaBi1 to sense stress, pausing replication to maintain genome integrity, and then allowing splicing immediately when permissive conditions return.
Collapse
Affiliation(s)
- Danielle S Kelley
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA
| | - Christopher W Lennon
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, 12222, USA
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA
| | - Michael R Miller
- Department of Chemistry, University at Albany, Albany, NY, 12222, USA
| | - Nilesh K Banavali
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA
| | - Hongmin Li
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA.
| | - Marlene Belfort
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, 12222, USA.
| |
Collapse
|