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The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons.

Simões J, Bezerra AR, Moura GR, Araújo H, Gut I, Bayes M, Santos MA - Front Microbiol (2016)

Bottom Line: In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons.Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains.Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.

View Article: PubMed Central - PubMed

Affiliation: Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal.

ABSTRACT
The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients, and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions, CUG sites incorporate leucine (3% of the times) and serine (97% of the times) on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT) strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.

No MeSH data available.


Related in: MedlinePlus

Total number of SNP by genomic region. ORFs (CDS, snoRNA, ncRNA, tRNA, and rRNA); Others (repeat-region, long-terminal repeat, retrotransposon, and centromeres); UTRs (blocked reading frame, snRNA, noncoding exon, and pseudogenes, 3′ UTR e 5′ UTR) and Out (regions not defined in ORFs, Others and UTRs). The data compares evolved and non-evolved strains.
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Figure 5: Total number of SNP by genomic region. ORFs (CDS, snoRNA, ncRNA, tRNA, and rRNA); Others (repeat-region, long-terminal repeat, retrotransposon, and centromeres); UTRs (blocked reading frame, snRNA, noncoding exon, and pseudogenes, 3′ UTR e 5′ UTR) and Out (regions not defined in ORFs, Others and UTRs). The data compares evolved and non-evolved strains.

Mentions: Comparison of evolved with corresponding non-evolved parental strains, showed sharp increase of total number of SNPs during evolution. 3827 SNPs were detected in the strain misreading the ACC-Thr codon and 12855 in the strain misreading the Leu (CTC) (Figure 5). The number of strain specific SNPs (unique SNPs) followed similar trends varying between 268 and 7352 SNPs in strains misreading ACC-Thr and CTC-Thr codons, respectively (Supplementary Figure 7). The genomic regions that revealed higher occurrence of SNPs per Kbp of genome are classified as “Others” and include repeat-regions, long-terminal repeats, retrotransposon, and centromeres. The genome region defined as “UTRs” which includes blocked reading frames, snRNA, noncoding exon, and pseudogenes, 3′ UTR and 5′ UTR, contained one SNP per 1.5–5.1 kbp. The genome regions designated as “ORFs” showed the lowest SNP content (1.7–8.1 Kbp). It includes CDS, snoRNA, ncRNA, tRNA, and rRNA (Supplementary Table 4). Regarding nucleotide substitutions in protein coding genes (Supplementary Table 5), non-synonymous nucleotide substitutions (dN) ranged from 0.33 in CTC-Leu and Ala (GCC) to 0.37 in the ATC-Ile misreading strains. On the other hand, synonymous nucleotide substitutions ranged from 0.91 in the strain misreading GGA-Gly to 1.24 in strain misreading CTC-Leu. The substitution rates at non-synonymous and synonymous sites (dN/dS ratio) ranged from 0.27 in the strain misreading the CTC-Leu codon to 0.4 in strain misreading the GGA-Gly codon, suggesting that these strains are under purifying selection and replacement substitutions are been purged by natural selection.


The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons.

Simões J, Bezerra AR, Moura GR, Araújo H, Gut I, Bayes M, Santos MA - Front Microbiol (2016)

Total number of SNP by genomic region. ORFs (CDS, snoRNA, ncRNA, tRNA, and rRNA); Others (repeat-region, long-terminal repeat, retrotransposon, and centromeres); UTRs (blocked reading frame, snRNA, noncoding exon, and pseudogenes, 3′ UTR e 5′ UTR) and Out (regions not defined in ORFs, Others and UTRs). The data compares evolved and non-evolved strains.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814463&req=5

Figure 5: Total number of SNP by genomic region. ORFs (CDS, snoRNA, ncRNA, tRNA, and rRNA); Others (repeat-region, long-terminal repeat, retrotransposon, and centromeres); UTRs (blocked reading frame, snRNA, noncoding exon, and pseudogenes, 3′ UTR e 5′ UTR) and Out (regions not defined in ORFs, Others and UTRs). The data compares evolved and non-evolved strains.
Mentions: Comparison of evolved with corresponding non-evolved parental strains, showed sharp increase of total number of SNPs during evolution. 3827 SNPs were detected in the strain misreading the ACC-Thr codon and 12855 in the strain misreading the Leu (CTC) (Figure 5). The number of strain specific SNPs (unique SNPs) followed similar trends varying between 268 and 7352 SNPs in strains misreading ACC-Thr and CTC-Thr codons, respectively (Supplementary Figure 7). The genomic regions that revealed higher occurrence of SNPs per Kbp of genome are classified as “Others” and include repeat-regions, long-terminal repeats, retrotransposon, and centromeres. The genome region defined as “UTRs” which includes blocked reading frames, snRNA, noncoding exon, and pseudogenes, 3′ UTR and 5′ UTR, contained one SNP per 1.5–5.1 kbp. The genome regions designated as “ORFs” showed the lowest SNP content (1.7–8.1 Kbp). It includes CDS, snoRNA, ncRNA, tRNA, and rRNA (Supplementary Table 4). Regarding nucleotide substitutions in protein coding genes (Supplementary Table 5), non-synonymous nucleotide substitutions (dN) ranged from 0.33 in CTC-Leu and Ala (GCC) to 0.37 in the ATC-Ile misreading strains. On the other hand, synonymous nucleotide substitutions ranged from 0.91 in the strain misreading GGA-Gly to 1.24 in strain misreading CTC-Leu. The substitution rates at non-synonymous and synonymous sites (dN/dS ratio) ranged from 0.27 in the strain misreading the CTC-Leu codon to 0.4 in strain misreading the GGA-Gly codon, suggesting that these strains are under purifying selection and replacement substitutions are been purged by natural selection.

Bottom Line: In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons.Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains.Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.

View Article: PubMed Central - PubMed

Affiliation: Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal.

ABSTRACT
The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients, and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions, CUG sites incorporate leucine (3% of the times) and serine (97% of the times) on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT) strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.

No MeSH data available.


Related in: MedlinePlus