Max A. B. Haase
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View article: Taxogenomic Analysis of a Novel Yeast Species, <i>Lachancea rosae</i> Sp. Nov. F.A., Isolated From the Wild Rose <i>Rosa californica</i>
Taxogenomic Analysis of a Novel Yeast Species, <i>Lachancea rosae</i> Sp. Nov. F.A., Isolated From the Wild Rose <i>Rosa californica</i> Open
A novel Saccharomycotina yeast strain, yHQL494, was isolated from the rose hip of the wild rose Rosa californica from Castle Crags State Park, California, USA. Phylogenetic analyses of both whole genome data and the sequences from the D1/D…
View article: Ancient co-option of LTR retrotransposons as yeast centromeres
Ancient co-option of LTR retrotransposons as yeast centromeres Open
Summary The evolutionary origins of the genetic point centromere in the brewer’s yeast Saccharomyces cerevisiae, a member of the order Saccharomycetales, are still unknown. Competing hypotheses suggest that the point centromere tripartite …
View article: macroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast
macroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast Open
In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones, providing additional layers of structural and epigenetic regulation. Here, we systematically replace individual replicative hu…
View article: Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts Open
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficienc…
View article: Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast <i>Hanseniaspora uvarum</i>
Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast <i>Hanseniaspora uvarum</i> Open
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 e…
View article: Supplemental materials for macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast
Supplemental materials for macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast Open
Associated supplemental files for the study entitled "macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast". Files include the uncropped HiC maps and the reference genome sequence of the histone shuffle s…
View article: Humanization reveals pervasive incompatibility of yeast and human kinetochore components
Humanization reveals pervasive incompatibility of yeast and human kinetochore components Open
Kinetochores assemble on centromeres to drive chromosome segregation in eukaryotic cells. Humans and budding yeast share most of the structural subunits of the kinetochore, whereas protein sequences have diverged considerably. The conserve…
View article: Manipulating the 3D organization of the largest synthetic yeast chromosome
Manipulating the 3D organization of the largest synthetic yeast chromosome Open
Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from ex…
View article: Taxogenomic analysis of a novel yeast species isolated from soil, <i>Pichia galeolata</i> sp. nov.
Taxogenomic analysis of a novel yeast species isolated from soil, <i>Pichia galeolata</i> sp. nov. Open
A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia . Strain yHMH…
View article: Context-dependent neocentromere activity in synthetic yeast chromosome VIII
Context-dependent neocentromere activity in synthetic yeast chromosome VIII Open
Pioneering advances in genome engineering, and specifically in genome writing, have revolutionized the field of synthetic biology, propelling us toward the creation of synthetic genomes. The Sc2.0 project aims to build the first fully synt…
View article: Engineered transcription-associated Cas9 targeting in eukaryotic cells
Engineered transcription-associated Cas9 targeting in eukaryotic cells Open
DNA targeting Class 2 CRISPR-Cas effector nucleases, including the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interactions that sequentially license their binding and cleavage activities at protospac…
View article: Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast<i>Hanseniaspora uvarum</i>
Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast<i>Hanseniaspora uvarum</i> Open
Across eukaryotic species, 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 understo…
View article: Genomic and ecological factors shaping specialism and generalism across an entire subphylum
Genomic and ecological factors shaping specialism and generalism across an entire subphylum Open
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth…
View article: Humanized nucleosomes reshape replication initiation and rDNA/nucleolar integrity in yeast
Humanized nucleosomes reshape replication initiation and rDNA/nucleolar integrity in yeast Open
Summary Eukaryotic DNA wraps around histone octamers forming nucleosomes, which modulate genome function by defining chromatin environments with distinct accessibility. These well-conserved properties allowed “humanization” of the nucleoso…
View article: Human macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast
Human macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast Open
Summary In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones providing additional layers of structural and epigenetic regulation. Here, we systematically replaced individual replic…
View article: Protein–protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning
Protein–protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning Open
The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer that protects the cell from external stressors, such as antibiotics. The Mla transport system is implicated in the Maintenance of OM Lipid Asymmetry by mediating re…
View article: Two differentially stable rDNA loci coexist on the same chromosome and form a single nucleolus
Two differentially stable rDNA loci coexist on the same chromosome and form a single nucleolus Open
The nucleolus is the most prominent membraneless compartment within the nucleus—dedicated to the metabolism of ribosomal RNA. Nucleoli are composed of hundreds of ribosomal DNA (rDNA) repeated genes that form large chromosomal clusters, wh…
View article: Protein-protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning
Protein-protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning Open
The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer that protects the cell from various external stressors, such as antibiotics. The Mla transport system is implicated in the M aintenance of outer membrane L ipid A s…
View article: DASH/Dam1 complex mutants stabilize ploidy by weakening kinetochore-microtubule attachments
DASH/Dam1 complex mutants stabilize ploidy by weakening kinetochore-microtubule attachments Open
Summary Forcing budding yeast to chromatinize their DNA with human histones manifests an abrupt fitness cost. We previously proposed chromosomal aneuploidy and missense mutations as two potential modes of adaptation to histone humanization…
View article: Stable twin rDNA loci form a single nucleolus in brewer’s yeast
Stable twin rDNA loci form a single nucleolus in brewer’s yeast Open
The nucleolus is the most prominent membraneless compartment within the nucleus 1, 2 - dedicated to the metabolism of ribosomal RNA. Nucleoli are composed of hundreds of ribosomal DNA (rDNA) repeated genes that form large chromosomal clust…
View article: Manipulating the 3D organization of the largest synthetic yeast chromosome
Manipulating the 3D organization of the largest synthetic yeast chromosome Open
Summary Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we report de novo synthe…
View article: Substrate, temperature, and geographical patterns among nearly 2000 natural yeast isolates
Substrate, temperature, and geographical patterns among nearly 2000 natural yeast isolates Open
Yeasts have broad importance as industrially and clinically relevant microbes and as powerful models for fundamental research, but we are only beginning to understand the roles yeasts play in natural ecosystems. Yeast ecology is often more…
View article: Substrate, temperature, and geographical patterns among nearly 2,000 natural yeast isolates
Substrate, temperature, and geographical patterns among nearly 2,000 natural yeast isolates Open
Yeasts have broad importance as industrially and clinically relevant microbes and as powerful models for fundamental research, but we are only beginning to understand the roles yeasts play in natural ecosystems. Yeast ecology is often more…
View article: Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples
Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples Open
Candida tropicalis is a human pathogen that primarily infects the immunocompromised. Whereas the genome of one isolate, C . tropicalis MYA-3404, was originally sequenced in 2009, there have been no large-scale, multi-isolate studies of the…
View article: Repeated horizontal gene transfer of <i>GAL</i> actose metabolism genes violates Dollo’s law of irreversible loss
Repeated horizontal gene transfer of <i>GAL</i> actose metabolism genes violates Dollo’s law of irreversible loss Open
Dollo’s law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic c…
View article: Repeated horizontal gene transfer of<i>GAL</i>actose metabolism genes violates Dollo’s law of irreversible loss
Repeated horizontal gene transfer of<i>GAL</i>actose metabolism genes violates Dollo’s law of irreversible loss Open
Dollo’s law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic c…
View article: Microbial Diversity Associated with the Pollen Stores of Captive-Bred Bumble Bee Colonies
Microbial Diversity Associated with the Pollen Stores of Captive-Bred Bumble Bee Colonies Open
The pollen stores of bumble bees host diverse microbiota that influence overall colony fitness. Yet, the taxonomic identity of these symbiotic microbes is relatively unknown. In this descriptive study, we characterized the microbial commun…