Project description:Over evolutionary timescales, the logic and pattern of cell-type specific gene expression can remain constant, yet the molecular mechanisms underlying such regulation can drift between alternative forms. Here, we document a new, especially clear example of this principle in the regulation of the haploid-specific genes across a wide group of fungal species. For most species, transcription of these genes is repressed in the a/ a cell type by a heterodimer of two homeodomain proteins, Mata1 and Mata2. We show that in the species Lachancea kluveri, repression of one haploid-specific gene (GPA1) requires, in addition to Mata1 and Mata2, a third regulatory protein, Mcm1. Model building, based on x-ray crystal structures of the three proteins, rationalizes the requirement for all three proteins: no single pair of the proteins is optimally arranged and we show that no single pair can bring about repression. Although the three-part solution is used to regulate GPA1 in L. kluveri, the other haploid specific genes in this species are regulated by the more conventional two-protein mechanism. This case study exemplifies the idea that the energy of DNA binding can be “shared out” in different ways and can result is different DNA-binding solutions across different genes—while maintaining the same pattern of gene expression.
Project description:Array data detailing the progression of DNA replication in the yeast Lachancea waltii. L. waltii cells were pregrown in heavy isotope medium and synchronized at early S phase. They were then released into normal medium, wherein DNA replication proceeds. Replicated DNA molecules are thus of heavy-light (HL) composition as compared to unreplicated molecules, which are heavy-heavy (HH). 4 time points were taken and the percent of heavy-light DNA was determined at each time point. The heavy-heavy and heavy-light DNA molecules were separated by ultracentrifugation, differentially labeled, and hybridized to a genomic array for L. waltii. The array thus shows the progression of DNA replication.
Project description:To understand the Sef1-dependent gene expression in Lachancea kluyveri under both fermentative and respiratory conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type and sef1 deletion mutant under both YPD and YPGly conditions.
Project description:To understand the iron-responsive gene expression in Lachancea kluyveri under high and low iron conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type, sef1 deletion, aft1 deletion and sef1aft1 double deletion mutants under the YPD+400mM ferrous iron and YPD+ 200 mM BPS conditions.
Project description:Over evolutionary timescales, the logic and pattern of cell-type specific gene expression can remain constant, yet the molecular mechanisms underlying such regulation can drift between alternative forms. Here, we document a new, especially clear example of this principle in the regulation of the haploid-specific genes across a wide group of fungal species. For most species, transcription of these genes is repressed in the a/ a cell type by a heterodimer of two homeodomain proteins, Mata1 and Mata2. We show that in the species Lachancea kluveri, repression of one haploid-specific gene (GPA1) requires, in addition to Mata1 and Mata2, a third regulatory protein, Mcm1. Model building, based on x-ray crystal structures of the three proteins, rationalizes the requirement for all three proteins: no single pair of the proteins is optimally arranged and we show that no single pair can bring about repression. Although the three-part solution is used to regulate GPA1 in L. kluveri, the other haploid specific genes in this species are regulated by the more conventional two-protein mechanism. This case study exemplifies the idea that the energy of DNA binding can be “shared out” in different ways and can result is different DNA-binding solutions across different genes—while maintaining the same pattern of gene expression.
Project description:In the frame of a multispecies project, Lachancea thermotolerans cells were treated with 5 mM sodium selenite. Cells were collected 10, 20, 30, 40, 50, 60, 70 and 80 minutes after the treatment and their transcriptomes were compared to those of mock-treated cultures. Four independent biological replicates were performed.
Project description:In the frame of a multispecies project, Lachancea kluyveri cells were treated with 5 mM sodium selenite. Cells were collected 10, 20, 30, 40, 50, 60, 70 and 80 minutes after the treatment and their transcriptomes were compared to those of mock-treated cultures. Four independent biological replicates were performed.