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López Hernández JF, Rubinstein BY, Unckless RL, Zanders SE. Modeling the evolution of Schizosaccharomyces pombe populations with multiple killer meiotic drivers. G3 (BETHESDA, MD.) 2024; 14:jkae142. [PMID: 38938172 DOI: 10.1093/g3journal/jkae142] [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: 05/23/2024] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
Meiotic drivers are selfish genetic loci that can be transmitted to more than half of the viable gametes produced by a heterozygote. This biased transmission gives meiotic drivers an evolutionary advantage that can allow them to spread over generations until all members of a population carry the driver. This evolutionary power can also be exploited to modify natural populations using synthetic drivers known as "gene drives." Recently, it has become clear that natural drivers can spread within genomes to birth multicopy gene families. To understand intragenomic spread of drivers, we model the evolution of 2 or more distinct meiotic drivers in a population. We employ the wtf killer meiotic drivers from Schizosaccharomyces pombe, which are multicopy in all sequenced isolates, as models. We find that a duplicate wtf driver identical to the parent gene can spread in a population unless, or until, the original driver is fixed. When the duplicate driver diverges to be distinct from the parent gene, we find that both drivers spread to fixation under most conditions, but both drivers can be lost under some conditions. Finally, we show that stronger drivers make weaker drivers go extinct in most, but not all, polymorphic populations with absolutely linked drivers. These results reveal the strong potential for natural meiotic drive loci to duplicate and diverge within genomes. Our findings also highlight duplication potential as a factor to consider in the design of synthetic gene drives.
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Affiliation(s)
| | - Boris Y Rubinstein
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Sarah E Zanders
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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Dang TTV, Maufrais C, Colin J, Moyrand F, Mouyna I, Coppée JY, Onyishi CU, Lipecka J, Guerrera IC, May RC, Janbon G. Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1. PLoS Biol 2024; 22:e3002724. [PMID: 39052688 PMCID: PMC11302930 DOI: 10.1371/journal.pbio.3002724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/06/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024] Open
Abstract
Alternative transcription start site (TSS) usage regulation has been identified as a major means of gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. Here, we first re-analyzed TSS-seq data to define genuine TSS clusters in 2 species of pathogenic Cryptococcus. We identified 2 types of TSS clusters associated with specific DNA sequence motifs. Our analysis also revealed that alternative TSS usage regulation in response to environmental cues is widespread in Cryptococcus, altering gene expression and protein targeting. Importantly, we performed a forward genetic screen to identify a unique transcription factor (TF) named Tur1, which regulates alternative TSS (altTSS) usage genome-wide when cells switch from exponential phase to stationary phase. ChiP-Seq and DamID-Seq analyses suggest that at some loci, the role of Tur1 might be direct. Tur1 has been previously shown to be essential for virulence in C. neoformans. We demonstrated here that a tur1Δ mutant strain is more sensitive to superoxide stress and phagocytosed more efficiently by macrophages than the wild-type (WT) strain.
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Affiliation(s)
- Thi Tuong Vi Dang
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Corinne Maufrais
- Université Paris Cité, Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, Paris, France
| | - Jessie Colin
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
- Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
| | - Frédérique Moyrand
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Isabelle Mouyna
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Jean-Yves Coppée
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Chinaemerem U. Onyishi
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Joanna Lipecka
- Université Paris Cité, SFR Necker INSERM US24/CNRS UAR3633, Proteomics Platform, Paris, France
| | - Ida Chiara Guerrera
- Université Paris Cité, SFR Necker INSERM US24/CNRS UAR3633, Proteomics Platform, Paris, France
| | - Robin C. May
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Guilhem Janbon
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
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Zheng JX, Du TY, Shao GC, Ma ZH, Jiang ZD, Hu W, Suo F, He W, Dong MQ, Du LL. Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers. Nat Commun 2023; 14:8334. [PMID: 38097609 PMCID: PMC10721834 DOI: 10.1038/s41467-023-44151-9] [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: 05/20/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. In several fission yeast species, single-gene KMDs belonging to the wtf gene family exert selfish killing by expressing a toxin and an antidote through alternative transcription initiation. Here we investigate how the toxin and antidote products of a wtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs PY motifs (Leu/Pro-Pro-X-Tyr) in its N-terminal cytosolic tail to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
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Affiliation(s)
- Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tong-Yang Du
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhu-Hui Ma
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wen Hu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wanzhong He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
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Jia GS, Zhang WC, Liang Y, Liu XH, Rhind N, Pidoux A, Brysch-Herzberg M, Du LL. A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus. G3 (BETHESDA, MD.) 2023; 13:jkad028. [PMID: 36748990 PMCID: PMC10085805 DOI: 10.1093/g3journal/jkad028] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and 3 other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5,098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these 2 species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of 2 types of mitochondrial selfish elements.
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Affiliation(s)
- Guo-Song Jia
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yue Liang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xi-Han Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alison Pidoux
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn 74081, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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Dang TTV, Colin J, Janbon G. Alternative Transcription Start Site Usage and Functional Implications in Pathogenic Fungi. J Fungi (Basel) 2022; 8:1044. [PMID: 36294609 PMCID: PMC9604717 DOI: 10.3390/jof8101044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/20/2022] Open
Abstract
Pathogenic fungi require delicate gene regulation mechanisms to adapt to diverse living environments and escape host immune systems. Recent advances in sequencing technology have exposed the complexity of the fungal genome, thus allowing the gradual disentanglement of multiple layers of gene expression control. Alternative transcription start site (aTSS) usage, previously reported to be prominent in mammals and to play important roles in physiopathology, is also present in fungi to fine-tune gene expression. Depending on the alteration in their sequences, RNA isoforms arising from aTSSs acquire different characteristics that significantly alter their stability and translational capacity as well as the properties and biologic functions of the resulting proteins. Disrupted control of aTSS usage has been reported to severely impair growth, virulence, and the infectious capacity of pathogenic fungi. Here, we discuss principle concepts, mechanisms, and the functional implication of aTSS usage in fungi.
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Affiliation(s)
- Thi Tuong Vi Dang
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Université de Paris Cité, F-75015 Paris, France
| | - Jessie Colin
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Université de Paris Cité, F-75015 Paris, France
- Ecole Pratique des Hautes Etudes, PSL Research University, F-75014 Paris, France
| | - Guilhem Janbon
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Université de Paris Cité, F-75015 Paris, France
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