Limits...
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

Gene ontology process terms. All genes affected by LOH regions of chromosome 2, 3, and R identified in the evolved strains. Data is relative to non-evolved strains. The graph represents the percentage of genes affected in each process above 10%.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4814463&req=5

Figure 4: Gene ontology process terms. All genes affected by LOH regions of chromosome 2, 3, and R identified in the evolved strains. Data is relative to non-evolved strains. The graph represents the percentage of genes affected in each process above 10%.

Mentions: To clarify if the proteome instability generated by the misreading tRNAs affected the genome, we have evolved the various strains for 100 generations and sequenced their genomes at the end of the evolution. Although read depth was relatively uniform across the genome in all strains, two evolved strains showed LOH relative to their unevolved progenitors. Indeed, strains misreading Leu CTC codons showed LOH in chromosome II (1,300,000–2,200,000) and chromosome III (100,000–900,000; Supplementary Figure 5), and the strain misreading the Ala-GCC codon showed LOH in chromosome R (300,000–1,500,000; Supplementary Figure 6). The affected region on chromosome II contains 428 ORFs, most of which are involved in unknown biological processes (28.3%), regulation of biological processes (19.9%), organelle organization (14.5%), transport (14.0%), and response to stress (14.0%; Figure 4). Noteworthy the cell adhesion process, which comprises 60 genes, was affected in 10 ORFs by this LOH. In chromosome III the affected region contains 357 ORFs. The majority of them are associated with unknown biological processes (32.8%), regulation of biological processes (18.5%), transport (14.6%), organelle organization (13.2%), and response to stress (12.6%). The affected region of chromosome R includes 560 ORFs and most of them are associated with unknown biological processes (27.3%), regulation of biological processes (21.8%), transport (16.6%), organelle organization (15.9%), and response to stress (13.2%).


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)

Gene ontology process terms. All genes affected by LOH regions of chromosome 2, 3, and R identified in the evolved strains. Data is relative to non-evolved strains. The graph represents the percentage of genes affected in each process above 10%.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Gene ontology process terms. All genes affected by LOH regions of chromosome 2, 3, and R identified in the evolved strains. Data is relative to non-evolved strains. The graph represents the percentage of genes affected in each process above 10%.
Mentions: To clarify if the proteome instability generated by the misreading tRNAs affected the genome, we have evolved the various strains for 100 generations and sequenced their genomes at the end of the evolution. Although read depth was relatively uniform across the genome in all strains, two evolved strains showed LOH relative to their unevolved progenitors. Indeed, strains misreading Leu CTC codons showed LOH in chromosome II (1,300,000–2,200,000) and chromosome III (100,000–900,000; Supplementary Figure 5), and the strain misreading the Ala-GCC codon showed LOH in chromosome R (300,000–1,500,000; Supplementary Figure 6). The affected region on chromosome II contains 428 ORFs, most of which are involved in unknown biological processes (28.3%), regulation of biological processes (19.9%), organelle organization (14.5%), transport (14.0%), and response to stress (14.0%; Figure 4). Noteworthy the cell adhesion process, which comprises 60 genes, was affected in 10 ORFs by this LOH. In chromosome III the affected region contains 357 ORFs. The majority of them are associated with unknown biological processes (32.8%), regulation of biological processes (18.5%), transport (14.6%), organelle organization (13.2%), and response to stress (12.6%). The affected region of chromosome R includes 560 ORFs and most of them are associated with unknown biological processes (27.3%), regulation of biological processes (21.8%), transport (16.6%), organelle organization (15.9%), and response to stress (13.2%).

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