Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum

• Published in: Genetics (Austin) 2024-03, Vol.226 (3)
• Main Authors: Haase, Max A B, Steenwyk, Jacob L, Boeke, Jef D
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Biological evolution; Cell cycle; Conserved sequence; DNA biosynthesis; Evolutionary conservation; Evolutionary genetics; Fungal Genetics and Genomics; Gene regulation; Genes; Genetic modification; Hanseniaspora; Hanseniaspora uvarum; Histones; Protein turnover; Regulatory mechanisms (biology); Regulatory sequences; Synthesis; Yeast; Yeasts
• ISSN: 1943-2631; 0016-6731; 1943-2631
• DOI: 10.1093/genetics/iyae008

Abstract Core histone genes display a remarkable diversity of cis-regulatory mechanisms despite their protein sequence conservation. However, the dynamics and significance of this regulatory turnover are not well understood. Here, we describe the evolutionary history of core histone gene regulation across 400 million years in budding yeasts. We find that canonical mode of core histone regulation—mediated by the trans-regulator Spt10—is ancient, likely emerging between 320 and 380 million years ago and is fixed in the majority of extant species. Unexpectedly, we uncovered the emergence of a novel core histone regulatory mode in the Hanseniaspora genus, from its fast-evolving lineage, which coincided with the loss of 1 copy of its paralogous core histone genes. We show that the ancestral Spt10 histone regulatory mode was replaced, via cis-regulatory changes in the histone control regions, by a derived Mcm1 histone regulatory mode and that this rewiring event occurred with no changes to the trans-regulator, Mcm1, itself. Finally, we studied the growth dynamics of the cell cycle and histone synthesis in genetically modified Hanseniaspora uvarum. We find that H. uvarum divides rapidly, with most cells completing a cell cycle within 60 minutes. Interestingly, we observed that the regulatory coupling between histone and DNA synthesis was lost in H. uvarum. Our results demonstrate that core histone gene regulation was fixed anciently in budding yeasts, however it has greatly diverged in the Hanseniaspora fast-evolving lineage. Hanseniaspora are a group of unicellular fungi primarily associated with vineyards and grape must. While much research has been conducted into their potential biotechnological applications, fewer studies have looked into their genetics and cell biology. Here, Haase, Steenwyk, and Boeke investigate the cell cycle progression and regulation of core histone genes in H. uvarum, revealing considerable differences to the well-known model yeast Saccharomyces cerevisiae.