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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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ClHst1 associates with the rDNA repeats.(A) Features of the three rDNA loci in C. lusitaniae are illustrated. The Pol I-transcribed 35S gene is processed to generate the 18S, 5.8S, and 25S rRNAs (arrows). The Pol III-transcribed 5S gene divides the non-transcribed spacer. All three loci occur near the ends of supercontigs, but only the right end of supercontig 3 has a telomere repeat (gray box), indicating the end of the chromosome. Vertical bars indicate the beginning (3L) or end (8R) of the supercontig sequence. (B) The association of ClHst1 across an rDNA repeat was examined by chromatin IP. Anti-myc antibody was used to immunoprecipitate proteins from ClHST1 (LRY2826) or ClHST1-MYC (LRY2858) yeast. The relative enrichment of each probe compared to a control locus, ClPRI2, is indicated.
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pgen-1003935-g001: ClHst1 associates with the rDNA repeats.(A) Features of the three rDNA loci in C. lusitaniae are illustrated. The Pol I-transcribed 35S gene is processed to generate the 18S, 5.8S, and 25S rRNAs (arrows). The Pol III-transcribed 5S gene divides the non-transcribed spacer. All three loci occur near the ends of supercontigs, but only the right end of supercontig 3 has a telomere repeat (gray box), indicating the end of the chromosome. Vertical bars indicate the beginning (3L) or end (8R) of the supercontig sequence. (B) The association of ClHst1 across an rDNA repeat was examined by chromatin IP. Anti-myc antibody was used to immunoprecipitate proteins from ClHST1 (LRY2826) or ClHST1-MYC (LRY2858) yeast. The relative enrichment of each probe compared to a control locus, ClPRI2, is indicated.

Mentions: Based on the properties of Sir2/Hst1 in S. cerevisiae, K. lactis, and S. pombe, it is expected that ClHst1 associates with the genomic loci at which it acts. Candidate loci include the rDNA repeats, subtelomeric regions, and promoters of repressed genes. C. lusitaniae lacks cryptic mating-type loci, which are sites of Sir2-mediated silencing in other species. To examine the candidate loci, the association of myc-tagged ClHst1 was examined by chromatin immunoprecipitation (IP). We first examined the repeated rRNA genes, which are annotated in three locations in the sequenced genome of C. lusitaniae. Three successive repeats are found on the left end of supercontig 3, one repeat with an additional 5S gene occurs on the right end of supercontig 3, and one repeat lacking a non-transcribed spacer is on the right end of supercontig 8 (Figure 1A). It is expected that the actual number of repeats at these loci is much greater, as S. cerevisiae encodes 100–200 tandem rRNA genes. Alignment of the three loci revealed significant variation in the non-transcribed spacers, NTS1 and NTS2. Because the rRNA genes at supercontig 3L are repeated in the assembly and display similarity among the non-transcribed spacers, this locus was selected as the template for primer design.


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)

ClHst1 associates with the rDNA repeats.(A) Features of the three rDNA loci in C. lusitaniae are illustrated. The Pol I-transcribed 35S gene is processed to generate the 18S, 5.8S, and 25S rRNAs (arrows). The Pol III-transcribed 5S gene divides the non-transcribed spacer. All three loci occur near the ends of supercontigs, but only the right end of supercontig 3 has a telomere repeat (gray box), indicating the end of the chromosome. Vertical bars indicate the beginning (3L) or end (8R) of the supercontig sequence. (B) The association of ClHst1 across an rDNA repeat was examined by chromatin IP. Anti-myc antibody was used to immunoprecipitate proteins from ClHST1 (LRY2826) or ClHST1-MYC (LRY2858) yeast. The relative enrichment of each probe compared to a control locus, ClPRI2, is indicated.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003935-g001: ClHst1 associates with the rDNA repeats.(A) Features of the three rDNA loci in C. lusitaniae are illustrated. The Pol I-transcribed 35S gene is processed to generate the 18S, 5.8S, and 25S rRNAs (arrows). The Pol III-transcribed 5S gene divides the non-transcribed spacer. All three loci occur near the ends of supercontigs, but only the right end of supercontig 3 has a telomere repeat (gray box), indicating the end of the chromosome. Vertical bars indicate the beginning (3L) or end (8R) of the supercontig sequence. (B) The association of ClHst1 across an rDNA repeat was examined by chromatin IP. Anti-myc antibody was used to immunoprecipitate proteins from ClHST1 (LRY2826) or ClHST1-MYC (LRY2858) yeast. The relative enrichment of each probe compared to a control locus, ClPRI2, is indicated.
Mentions: Based on the properties of Sir2/Hst1 in S. cerevisiae, K. lactis, and S. pombe, it is expected that ClHst1 associates with the genomic loci at which it acts. Candidate loci include the rDNA repeats, subtelomeric regions, and promoters of repressed genes. C. lusitaniae lacks cryptic mating-type loci, which are sites of Sir2-mediated silencing in other species. To examine the candidate loci, the association of myc-tagged ClHst1 was examined by chromatin immunoprecipitation (IP). We first examined the repeated rRNA genes, which are annotated in three locations in the sequenced genome of C. lusitaniae. Three successive repeats are found on the left end of supercontig 3, one repeat with an additional 5S gene occurs on the right end of supercontig 3, and one repeat lacking a non-transcribed spacer is on the right end of supercontig 8 (Figure 1A). It is expected that the actual number of repeats at these loci is much greater, as S. cerevisiae encodes 100–200 tandem rRNA genes. Alignment of the three loci revealed significant variation in the non-transcribed spacers, NTS1 and NTS2. Because the rRNA genes at supercontig 3L are repeated in the assembly and display similarity among the non-transcribed spacers, this locus was selected as the template for primer design.

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