Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid

Dandage, Rohan; Berger, Caroline M.; Gagnon‐Arsenault, Isabelle; Moon, Kyung Mee; Stacey, R. Greg; Foster, Leonard J.; Landry, Christian R.

doi:10.1093/molbev/msaa298

Cited by 13 publications

(8 citation statements)

References 69 publications

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“…Because hybridization combines two diverged genomes into a single organism, hybrids can face a suite of challenges, from reconciling protein interactions at the cellular level ( Sloan et al, 2017 ; Dandage et al, 2021 ; Piatkowska et al, 2013 ) to targeting the appropriate ecological niche at the organismal level ( Arnegard et al, 2014 ). Although we know that reconciling these challenges often involves changes in ancestry at genes and regulatory regions ( Principle 2 ), we rarely know the mechanisms that act to drive these changes.…”

Section: From Pattern To Process: Genome Evolution After Hybridization Is Shaped By Diverse Evolutionary Forcesmentioning

confidence: 99%

The genomic consequences of hybridization

Moran

Payne

Langdon

et al. 2021

eLife

194

189

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In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.

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Section: From Pattern To Process: Genome Evolution After Hybridization Is Shaped By Diverse Evolutionary Forcesmentioning

confidence: 99%

The genomic consequences of hybridization

Moran

Payne

Langdon

et al. 2021

eLife

194

189

View full text Add to dashboard Cite

show abstract

“…Cross interactions between paralogous modules are common in newly formed yeast hybrids, even when parental species have diverged over 50 million years 36 . Tightly-interacting modules may be subject to dominant negative effects due to mutations in their paralogous partners, suggesting doublets involving highly interacting proteins are more likely to revert to singletons.…”

Section: Resultsmentioning

confidence: 99%

Genome doubling enabled the expansion of yeast vesicle traffic pathways

Purkanti

Thattai

2022

Sci Rep

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Vesicle budding and fusion in eukaryotes depend on a suite of protein types, such as Arfs, Rabs, coats and SNAREs. Distinct paralogs of these proteins act at distinct intracellular locations, suggesting a link between gene duplication and the expansion of vesicle traffic pathways. Genome doubling, a common source of paralogous genes in fungi, provides an ideal setting in which to explore this link. Here we trace the fates of paralog doublets derived from the 100-Ma-old hybridization event that gave rise to the whole genome duplication clade of budding yeast. We find that paralog doublets involved in specific vesicle traffic functions and pathways are convergently retained across the entire clade. Vesicle coats and adaptors involved in secretory and early-endocytic pathways are retained as doublets, at rates several-fold higher than expected by chance. Proteins involved in later endocytic steps and intra-Golgi traffic, including the entire set of multi-subunit and coiled-coil tethers, have reverted to singletons. These patterns demonstrate that selection has acted to expand and diversify the yeast vesicle traffic apparatus, across species and time.

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“…However, it is not sufficient. Cross interactions between paralogous modules are common in newly formed yeast hybrids, even when parental species have diverged over 50 million years [46]. Tightly-interacting modules may be subject to dominant negative effects due to mutations in their paralogous partners, perhaps explaining why we see a weak association between interaction degree and doublet loss.…”

Section: Protein Interactions Influence the Evolution Of Modulesmentioning

confidence: 89%

Paralogous gene modules derived from ancient hybridization drive vesicle traffic evolution in yeast

Purkanti

Thattai

2021

Preprint

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Modules of interacting proteins regulate vesicle budding and fusion in eukaryotes. Distinct paralogous copies of these modules act at distinct sub-cellular locations. The processes by which such large gene modules are duplicated and retained remain unclear. Here we show that interspecies hybridization is a potent source of paralogous gene modules. We study the dynamics of paralog doublets derived from the 100-million-year-old hybridization event that gave rise to the whole genome duplication clade of budding yeast. We show that paralog doublets encoding vesicle traffic proteins are convergently retained across species. Vesicle coats and adaptors involved in secretory and early-endocytic pathways are retained as doublets, while tethers and other machinery involved in intra-Golgi traffic and later endocytic steps are reduced to singletons. These patterns reveal common selective pressures that have sculpted traffic pathways in diverse yeast species. They suggest that hybridization may have played a pivotal role in the expansion of the endomembrane system.

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Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid

Cited by 13 publications

References 69 publications

The genomic consequences of hybridization

The genomic consequences of hybridization

Genome doubling enabled the expansion of yeast vesicle traffic pathways

Paralogous gene modules derived from ancient hybridization drive vesicle traffic evolution in yeast

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