The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family
- UCD Conway Institute and School of Medicine, University College Dublin, Ireland
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, France
Figures
Figure 1 with 1 supplement
Genomic organization and domain structure of WHO genes.
(A) Polymorphic clusters of WHO genes and pseudogenes downstream of FBA1 in Torulaspora species. Multiple alleles are shown for T. delbrueckii, T. pretoriensis, and T. globosa. WHO genes are …
Figure 1—figure supplement 1
Genomic organization and domain structure of WHO genes in Lachancea species.
(A) WHO genes and pseudogenes downstream of FBA1 in Lachancea species. Fragments of the 3’ end of FBA1 are marked. For WHO genes, ‘int’ indicates an intact gene, ‘ψ” indicates a substantial …
Figure 2
WHO6 induces allele-specific DNA cleavage of the T. delbrueckii FBA1 gene, with DNA repair by gene conversion or NHEJ.
(A) Summary of the experiment. Haploid S. cerevisiae strains, containing a non-expressed T. delbrueckii FBA1 ORF (TdFBA1-S or TdFBA1-R alleles) integrated at ADE2, were transformed multiple …
Figure 3
Different evolutionary dynamics of the 5’ and 3’ parts of T. delbrueckii FBA1.
(A) Heatmap showing regions of nucleotide sequence diversity (π) among 15 sequenced FBA1 alleles from T. delbrueckii isolates, plotted in 10 bp windows. (B) Inconsistency of phylogenetic trees …
Figure 4
Proposed mechanism of WHO element homing.
(A) Similarity of mechanisms of action of WHO, VDE and HO. The mechanism we propose for WHO elements integrating at FBA1 is compared to the known mechanisms for VDE integrating into VMA1 and for HO-…
Figure 5 with 1 supplement
Families of WHO genes and their phylogenetic relationship to HO and VDE.
Magenta branches indicate WHO genes that are located at the FBA1 locus, and blue branches indicate WHO genes that are not beside FBA1. 14 WHO families are marked by brackets. Individual WHO gene …
Figure 5—figure supplement 1
Some Kazachstania species have an intron in FBA1 at a location corresponding to the WHO cleavage site in Torulaspora.
(A) Genome organization around FBA1 in Kazachstania servazzii and its close relatives. Data from 4 strains of K. servazzii are shown. FBA1 genes, exons and fragments are colored magenta and their …
Figure 6
WHO10 is an active mobile genetic element in T. globosa and integrates into loci other than FBA1.
Each panel shows a pair of allelic regions from T. globosa strains CBS2947 and CBS764T. Intact WHO10 genes are shown in green, FBA1 fragments in magenta, and host genes in blue. (A-E) Five …
Figure 7
Model for the origin of HO by domestication of a WHO element.
See Discussion for details. The dashed arrows indicate two possible routes to HO, from ancestral WHO elements that either were, or were not, specifically associated with FBA1.
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Torulaspora delbrueckii) | FBA1 | Gordon et al., 2011 | TDEL0B06660; NCBI: XM_003679958 | Strain CBS1146; TdFBA1-S allele |
| Strain, strain background (Saccharomyces cerevisiae) | IMX585 | Mans et al., 2015 | S. cerevisiae strain with integrated CAS9 gene | |
| Strain, strain background (Torulaspora delbrueckii) | L09; L10; L11; L12; L13; L15; L16; L18; L19; L20 | This paper | Strain collection of Lallemand, Inc | |
| Strain, strain background (Torulaspora delbrueckii) | NCYC696 | National Collection of Yeast Cultures (UK) | ||
| Strain, strain background (multiple Torulaspora species) | All CBS strains | Westerdijk Fungal Biodiversity Institute (Netherlands) | ||
| Strain, strain background (Torulaspora pretoriensis) | UWOPS 83–1046.2 | MA Lachance, University of Western Ontario (Canada) | ||
| Strain, strain background (Zygotorulaspora mrakii) | NRRL Y-6702 | CP Kurtzman, USDA Agricultural Research Service | ||
| Strain, strain background (Naumovozyma castellii) | Y056 (NRRL Y-12630T); Y174 (CBS4310); Y287 (CBS3006); Y668 (CBS1579) | Jure Piškur, Lund University (Sweden) | See Spírek et al., 2003 | |
| Recombinant DNA reagent | pMEL13 plasmid | Mans et al., 2015 | ||
| Sequence-based reagent | ADE2.Y sgRNA template | DiCarlo et al., 2013 | ||
| Recombinant DNA reagent | pIL75-KanMX plasmid | Liachko and Dunham, 2014 | ||
| Recombinant DNA reagent | pWHO6 | This paper | DNA sequence is in Supplementary file 3 | |
| Recombinant DNA reagent | pWHO6-HA | This paper | DNA sequence is in Supplementary file 3 | |
| Recombinant DNA reagent | pGFP-HA | This paper | DNA sequence is in Supplementary file 3 | |
| Sequence-based reagent | Sc ade2::TdFBA1-S repair template | This paper | DNA sequence is in Supplementary file 3 | |
| Sequence-based reagent | Sc ade2::TdFBA1-R repair template | This paper | DNA sequence is in Supplementary file 3 | |
| Sequence-based reagent | Primers for PCR of Sc ade2::TdFBA1 locus | This paper | 5’-TGACCACGTT AATGGCTCC-3’ and 5’-CACCAGCTCCA GCGATAATTG-3’ | |
| Software, algorithm | SPAdes assembler | Bankevich et al., 2012 | V3.11.1 | RRID:SCR_000131 |
| Software, algorithm | HGAP3 assembler | Chin et al., 2013 |
Additional files
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Supplementary file 1
T. delbrueckii genome sequence data used in this study.
- https://cdn.elifesciences.org/articles/55336/elife-55336-supp1-v2.docx
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Supplementary file 2
Other genome sequence data used in this study.
- https://cdn.elifesciences.org/articles/55336/elife-55336-supp2-v2.docx
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Supplementary file 3
Sequences of the plasmids pWHO6, pWHO6-HA and pGFP-HA, and of the ade2::TdFBA1-S and ade2::TdFBA1-R constructs.
- https://cdn.elifesciences.org/articles/55336/elife-55336-supp3-v2.txt
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Transparent reporting form
- https://cdn.elifesciences.org/articles/55336/elife-55336-transrepform-v2.docx
