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Genome-wide replication landscape of Candida glabrata.

Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF - BMC Biol. (2015)

Bottom Line: Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata.No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), F-75015, Paris, France. stephane.descorps-declere@pasteur.fr.

ABSTRACT

Background: The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments.

Results: We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.

Conclusions: Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.

No MeSH data available.


Related in: MedlinePlus

ARS consensus sequences. aC. glabrata ACS determined from the whole set of 275 ARSs (top), or from the 83 bona fide origins (bottom). Boundaries of the element are clearly visible in the latter case. The three positions differing from the S. cerevisiae ACS are shown by orange arrows. The WTW trinucleotide was barely detected. bS. cerevisiae ACS determined from the set of 337 known ARSs listed in the Saccharomyces Genome Database (SGD) [70] (top), or from the 274 ARSs identified here (bottom). Boundaries of the canonical ACS [10] or of the extended ACS (EACS) are indicated, as well as the B1 box and WTW trinucleotide [38]. Note that although the ACS identified in the ARS capture experiment was closer to the C. glabrata ACS than to the S. cerevisiae canonical ACS, the requirement for the B1 box was greater in S. cerevisiae than in C. glabrata. c Alignment of ARS_F6 with the ARS identified by Zordan et al. [46], showing 48 bp in common between the two sequences. The ACS is shown in red. ACS ARS consensus sequence, ARS autonomously replicating sequence
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Fig6: ARS consensus sequences. aC. glabrata ACS determined from the whole set of 275 ARSs (top), or from the 83 bona fide origins (bottom). Boundaries of the element are clearly visible in the latter case. The three positions differing from the S. cerevisiae ACS are shown by orange arrows. The WTW trinucleotide was barely detected. bS. cerevisiae ACS determined from the set of 337 known ARSs listed in the Saccharomyces Genome Database (SGD) [70] (top), or from the 274 ARSs identified here (bottom). Boundaries of the canonical ACS [10] or of the extended ACS (EACS) are indicated, as well as the B1 box and WTW trinucleotide [38]. Note that although the ACS identified in the ARS capture experiment was closer to the C. glabrata ACS than to the S. cerevisiae canonical ACS, the requirement for the B1 box was greater in S. cerevisiae than in C. glabrata. c Alignment of ARS_F6 with the ARS identified by Zordan et al. [46], showing 48 bp in common between the two sequences. The ACS is shown in red. ACS ARS consensus sequence, ARS autonomously replicating sequence

Mentions: Using the motif finder GIMSAN, we identified a 17-bp A/T-rich ARS consensus sequence (ACS) common to the 275 DNA fragments selected (Fig. 6a). This ACS is similar to the core S. cerevisiae 11-bp ACS [10] and the 17-bp extended ACS [38], except for slight differences on three positions. When only the set of 83 bona fide origins was considered, a nearly identical motif was detected, with boundaries clearly visible (Fig. 6a). The same analysis was performed with ARSs extracted from S. cerevisiae. The motif detected was closer to the C. glabrata ACS than to the canonical S. cerevisiae ACS (Fig. 5b). However, when the B1 sequence was considered, particularly the WTW trinucleotide [38], it was found to be more conserved in ARSs replicating in S. cerevisiae than in ARSs replicating in C. glabrata. Altogether these observations strongly suggest that the requirement for the B1 box is weaker in C. glabrata, and that the information necessary to initiate replication is mostly contained in the 17 bp ACS, in which some positions are more constrained than in the S. cerevisiae ACS.Fig. 6


Genome-wide replication landscape of Candida glabrata.

Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF - BMC Biol. (2015)

ARS consensus sequences. aC. glabrata ACS determined from the whole set of 275 ARSs (top), or from the 83 bona fide origins (bottom). Boundaries of the element are clearly visible in the latter case. The three positions differing from the S. cerevisiae ACS are shown by orange arrows. The WTW trinucleotide was barely detected. bS. cerevisiae ACS determined from the set of 337 known ARSs listed in the Saccharomyces Genome Database (SGD) [70] (top), or from the 274 ARSs identified here (bottom). Boundaries of the canonical ACS [10] or of the extended ACS (EACS) are indicated, as well as the B1 box and WTW trinucleotide [38]. Note that although the ACS identified in the ARS capture experiment was closer to the C. glabrata ACS than to the S. cerevisiae canonical ACS, the requirement for the B1 box was greater in S. cerevisiae than in C. glabrata. c Alignment of ARS_F6 with the ARS identified by Zordan et al. [46], showing 48 bp in common between the two sequences. The ACS is shown in red. ACS ARS consensus sequence, ARS autonomously replicating sequence
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Related In: Results  -  Collection

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Fig6: ARS consensus sequences. aC. glabrata ACS determined from the whole set of 275 ARSs (top), or from the 83 bona fide origins (bottom). Boundaries of the element are clearly visible in the latter case. The three positions differing from the S. cerevisiae ACS are shown by orange arrows. The WTW trinucleotide was barely detected. bS. cerevisiae ACS determined from the set of 337 known ARSs listed in the Saccharomyces Genome Database (SGD) [70] (top), or from the 274 ARSs identified here (bottom). Boundaries of the canonical ACS [10] or of the extended ACS (EACS) are indicated, as well as the B1 box and WTW trinucleotide [38]. Note that although the ACS identified in the ARS capture experiment was closer to the C. glabrata ACS than to the S. cerevisiae canonical ACS, the requirement for the B1 box was greater in S. cerevisiae than in C. glabrata. c Alignment of ARS_F6 with the ARS identified by Zordan et al. [46], showing 48 bp in common between the two sequences. The ACS is shown in red. ACS ARS consensus sequence, ARS autonomously replicating sequence
Mentions: Using the motif finder GIMSAN, we identified a 17-bp A/T-rich ARS consensus sequence (ACS) common to the 275 DNA fragments selected (Fig. 6a). This ACS is similar to the core S. cerevisiae 11-bp ACS [10] and the 17-bp extended ACS [38], except for slight differences on three positions. When only the set of 83 bona fide origins was considered, a nearly identical motif was detected, with boundaries clearly visible (Fig. 6a). The same analysis was performed with ARSs extracted from S. cerevisiae. The motif detected was closer to the C. glabrata ACS than to the canonical S. cerevisiae ACS (Fig. 5b). However, when the B1 sequence was considered, particularly the WTW trinucleotide [38], it was found to be more conserved in ARSs replicating in S. cerevisiae than in ARSs replicating in C. glabrata. Altogether these observations strongly suggest that the requirement for the B1 box is weaker in C. glabrata, and that the information necessary to initiate replication is mostly contained in the 17 bp ACS, in which some positions are more constrained than in the S. cerevisiae ACS.Fig. 6

Bottom Line: Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata.No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), F-75015, Paris, France. stephane.descorps-declere@pasteur.fr.

ABSTRACT

Background: The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments.

Results: We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.

Conclusions: Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.

No MeSH data available.


Related in: MedlinePlus