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The deacetylase Sir2 from the yeast Clavispora lusitaniae lacks the evolutionarily conserved capacity to generate subtelomeric heterochromatin.

Froyd CA, Kapoor S, Dietrich F, Rusche LN - PLoS Genet. (2013)

Bottom Line: However, we found no evidence that ClHst1 associates with subtelomeric regions or impacts gene expression directly.After subsequent species diversification, the SIR2 paralog was apparently lost in the C. lusitaniae lineage.Thus, C. lusitaniae presents an opportunity to discover how subtelomeric chromatin can be reconfigured.

View Article: PubMed Central - PubMed

Affiliation: Biochemistry Department, Duke University, Durham, North Carolina, United States of America.

ABSTRACT
Deacetylases of the Sir2 or sirtuin family are thought to regulate life cycle progression and life span in response to nutrient availability. This family has undergone successive rounds of duplication and diversification, enabling the enzymes to perform a wide variety of biological functions. Two evolutionarily conserved functions of yeast Sir2 proteins are the generation of repressive chromatin in subtelomeric domains and the suppression of unbalanced recombination within the tandem rDNA array. Here, we describe the function of the Sir2 ortholog ClHst1 in the yeast Clavispora lusitaniae, an occasional opportunistic pathogen. ClHst1 was localized to the non-transcribed spacer regions of the rDNA repeats and deacetylated histones at these loci, indicating that, like other Sir2 proteins, ClHst1 modulates chromatin structure at the rDNA repeats. However, we found no evidence that ClHst1 associates with subtelomeric regions or impacts gene expression directly. This surprising observation highlights the plasticity of sirtuin function. Related yeast species, including Candida albicans, possess an additional Sir2 family member. Thus, it is likely that the ancestral Candida SIR2/HST1 gene was duplicated and subfunctionalized, such that HST1 retained the capacity to regulate rDNA whereas SIR2 had other functions, perhaps including the generation of subtelomeric chromatin. After subsequent species diversification, the SIR2 paralog was apparently lost in the C. lusitaniae lineage. Thus, C. lusitaniae presents an opportunity to discover how subtelomeric chromatin can be reconfigured.

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Expression of subtelomeric genes did not change in the absence of ClHst1.Average normalized read counts are plotted for all genes within 40,000 base pairs of a telomere repeat sequence. These genes are located on contigs 2L, 4R, 5L, 7L, and 7R. For each gene, the distance of the start codon from the telomere repeat sequence is plotted on the x-axis. The dashed rectangle in the upper panel is expanded in the lower panel. Strains examined were wild-type (LRY2544; open boxes) and hst1Δ (LRY2623 and LRY2671; shaded diamonds).
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pgen-1003935-g006: Expression of subtelomeric genes did not change in the absence of ClHst1.Average normalized read counts are plotted for all genes within 40,000 base pairs of a telomere repeat sequence. These genes are located on contigs 2L, 4R, 5L, 7L, and 7R. For each gene, the distance of the start codon from the telomere repeat sequence is plotted on the x-axis. The dashed rectangle in the upper panel is expanded in the lower panel. Strains examined were wild-type (LRY2544; open boxes) and hst1Δ (LRY2623 and LRY2671; shaded diamonds).

Mentions: Unlike ClHst1, Sir2 orthologs in S. cerevisiae and K. lactis are associated with telomeres, and consequently subtelomeric genes are induced in the absence of these proteins. To confirm the absence of ClHst1 at telomeres, we compared the expression of subtelomeric genes in wild-type and hst1Δ C. lusitaniae cells. If ClHst1 is indeed absent from the telomeres, no change in expression of subtelomeric genes is expected. RNA was isolated from two independently constructed Clhst1Δ strains as well as the parental wild-type ClHST1 strain, and cDNA was prepared for Illumina sequencing. The normalized number of reads derived from each gene was compared in Clhst1Δ and wild-type strains. All genes within 40 kbp of a telomere repeat sequence were examined, and none were found to differ by more than two-fold (Figure 6). Of the seven genes located elsewhere that were induced, CLUG_02300 is 2 kbp from the end of a supercontig lacking telomere repeats, and CLUG_01197 is 24 kbp from an end. However, neither gene displayed properties consistent with being silenced by block of Hst1-mediated heterochromatin. CLUG_01197 was well-expressed even in the presence of ClHst1, whereas CLUG_02300 remained poorly expressed in the absence of ClHst1 (Figure S2). Moreover, neighboring genes did not share the expression patterns of these two genes. Therefore, the gene expression data are consistent with the absence of ClHst1 at telomeres.


The deacetylase Sir2 from the yeast Clavispora lusitaniae lacks the evolutionarily conserved capacity to generate subtelomeric heterochromatin.

Froyd CA, Kapoor S, Dietrich F, Rusche LN - PLoS Genet. (2013)

Expression of subtelomeric genes did not change in the absence of ClHst1.Average normalized read counts are plotted for all genes within 40,000 base pairs of a telomere repeat sequence. These genes are located on contigs 2L, 4R, 5L, 7L, and 7R. For each gene, the distance of the start codon from the telomere repeat sequence is plotted on the x-axis. The dashed rectangle in the upper panel is expanded in the lower panel. Strains examined were wild-type (LRY2544; open boxes) and hst1Δ (LRY2623 and LRY2671; shaded diamonds).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814328&req=5

pgen-1003935-g006: Expression of subtelomeric genes did not change in the absence of ClHst1.Average normalized read counts are plotted for all genes within 40,000 base pairs of a telomere repeat sequence. These genes are located on contigs 2L, 4R, 5L, 7L, and 7R. For each gene, the distance of the start codon from the telomere repeat sequence is plotted on the x-axis. The dashed rectangle in the upper panel is expanded in the lower panel. Strains examined were wild-type (LRY2544; open boxes) and hst1Δ (LRY2623 and LRY2671; shaded diamonds).
Mentions: Unlike ClHst1, Sir2 orthologs in S. cerevisiae and K. lactis are associated with telomeres, and consequently subtelomeric genes are induced in the absence of these proteins. To confirm the absence of ClHst1 at telomeres, we compared the expression of subtelomeric genes in wild-type and hst1Δ C. lusitaniae cells. If ClHst1 is indeed absent from the telomeres, no change in expression of subtelomeric genes is expected. RNA was isolated from two independently constructed Clhst1Δ strains as well as the parental wild-type ClHST1 strain, and cDNA was prepared for Illumina sequencing. The normalized number of reads derived from each gene was compared in Clhst1Δ and wild-type strains. All genes within 40 kbp of a telomere repeat sequence were examined, and none were found to differ by more than two-fold (Figure 6). Of the seven genes located elsewhere that were induced, CLUG_02300 is 2 kbp from the end of a supercontig lacking telomere repeats, and CLUG_01197 is 24 kbp from an end. However, neither gene displayed properties consistent with being silenced by block of Hst1-mediated heterochromatin. CLUG_01197 was well-expressed even in the presence of ClHst1, whereas CLUG_02300 remained poorly expressed in the absence of ClHst1 (Figure S2). Moreover, neighboring genes did not share the expression patterns of these two genes. Therefore, the gene expression data are consistent with the absence of ClHst1 at telomeres.

Bottom Line: However, we found no evidence that ClHst1 associates with subtelomeric regions or impacts gene expression directly.After subsequent species diversification, the SIR2 paralog was apparently lost in the C. lusitaniae lineage.Thus, C. lusitaniae presents an opportunity to discover how subtelomeric chromatin can be reconfigured.

View Article: PubMed Central - PubMed

Affiliation: Biochemistry Department, Duke University, Durham, North Carolina, United States of America.

ABSTRACT
Deacetylases of the Sir2 or sirtuin family are thought to regulate life cycle progression and life span in response to nutrient availability. This family has undergone successive rounds of duplication and diversification, enabling the enzymes to perform a wide variety of biological functions. Two evolutionarily conserved functions of yeast Sir2 proteins are the generation of repressive chromatin in subtelomeric domains and the suppression of unbalanced recombination within the tandem rDNA array. Here, we describe the function of the Sir2 ortholog ClHst1 in the yeast Clavispora lusitaniae, an occasional opportunistic pathogen. ClHst1 was localized to the non-transcribed spacer regions of the rDNA repeats and deacetylated histones at these loci, indicating that, like other Sir2 proteins, ClHst1 modulates chromatin structure at the rDNA repeats. However, we found no evidence that ClHst1 associates with subtelomeric regions or impacts gene expression directly. This surprising observation highlights the plasticity of sirtuin function. Related yeast species, including Candida albicans, possess an additional Sir2 family member. Thus, it is likely that the ancestral Candida SIR2/HST1 gene was duplicated and subfunctionalized, such that HST1 retained the capacity to regulate rDNA whereas SIR2 had other functions, perhaps including the generation of subtelomeric chromatin. After subsequent species diversification, the SIR2 paralog was apparently lost in the C. lusitaniae lineage. Thus, C. lusitaniae presents an opportunity to discover how subtelomeric chromatin can be reconfigured.

Show MeSH
Related in: MedlinePlus