A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans

Gomes, Ana Catarina; Miranda, Isabel M.; Silva, Raquel M.; Moura, Gabriela; Thomas, Benjamin; Akoulitchev, Alexandre; Santos, Manuel A. S.

doi:10.1186/gb-2007-8-10-r206

Cited by 107 publications

(154 citation statements)

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“…To increase Leu misincorporation at CUG sites, we have inserted one (strain T1) or two (strain T2) copies of a yeast Leu tDNA CAG Leu gene (25) into the RPS10 genome locus of the Candida albicans SN148 strain (26). This heterologous tRNA CAG Leu misincorporates Leu only at the atypical C. albicans Ser CUGs (23,25). We also knocked out one or two copies of the chromosomal C. albicans Ser tRNA CAG Ser gene in strains T1 and T2, producing strains T1KO1 and T2KO1 or T2KO2 (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Protein X-ray crystallography and molecular modeling showed that the Leu and Ser residues encoded by CUGs are partially exposed to the solvent or on the interface of subunits of protein complexes where they can be better tolerated (24). These structural data explain the high tolerance to CUG ambiguity (23) and are fundamental to rationalize the evolution of CUG reassignment in the fungal CTG clade. However, the dynamic range of Leu misincorporation at CUGs and the selective advantages that it spawns are not fully understood.…”

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confidence: 99%

“…Remarkably, these fungi still incorporate Ser (∼97%) and Leu (∼3%) at thousands of CUG sites present in over 60% of their genes (23). Protein X-ray crystallography and molecular modeling showed that the Leu and Ser residues encoded by CUGs are partially exposed to the solvent or on the interface of subunits of protein complexes where they can be better tolerated (24).…”

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Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification

Bezerra

Simões

Lee

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

110

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Many fungi restructured their proteomes through incorporation of serine (Ser) at thousands of protein sites coded by the leucine (Leu) CUG codon. How these fungi survived this potentially lethal genetic code alteration and its relevance for their biology are not understood. Interestingly, the human pathogen Candida albicans maintains variable Ser and Leu incorporation levels at CUG sites, suggesting that this atypical codon assignment flexibility provided an effective mechanism to alter the genetic code. To test this hypothesis, we have engineered C. albicans strains to misincorporate increasing levels of Leu at protein CUG sites. Tolerance to the misincorporations was very high, and one strain accommodated the complete reversion of CUG identity from Ser back to Leu. Increasing levels of Leu misincorporation decreased growth rate, but production of phenotypic diversity on a phenotypic array probing various metabolic networks, drug resistance, and host immune cell responses was impressive. Genome resequencing revealed an increasing number of genotype changes at polymorphic sites compared with the control strain, and 80% of Leu misincorporation resulted in complete loss of heterozygosity in a large region of chromosome V. The data unveil unanticipated links between gene translational fidelity, proteome instability and variability, genome diversification, and adaptive phenotypic diversity. They also explain the high heterozygosity of the C. albicans genome and open the door to produce microorganisms with genetic code alterations for basic and applied research.codon reassignment | evolution | tRNA N atural alterations to the standard genetic code have been discovered in Mycoplasma (1, 2), Micrococci (3), ciliates (4), fungi (5, 6), and mitochondria (7), modifying the hypothesis of a universal genetic code (8). Both neutral (9) and nonneutral theories (10) have been proposed to explain codon reassignments; however, experimental data to support or refute them are scarce, and genetic code alterations remain an intriguing biological puzzle. Despite this fact, it is becoming clear that genetic code alterations are associated with mutations in tRNAs and translation release factors that expand or restrict codon decoding capacity (7). In other words, alterations of translational factors have the potential to release the genetic code from its frozen state. This hypothesis is strongly supported by the widespread cotranslational incorporation of selenocysteine into the active site of selenoprotein (11) and pyrrolysine in the active site of the methyltransferases of several Metanosarcina species (12), Desulfitobacterium hafniense (13), and the gutless worm Olavius algarvensis (14). The selective advantages produced by these two amino acids are associated with evolution of proteins with unique catalytic properties.The flexibility of the genetic code is further highlighted by the in vivo incorporation of artificial amino acids into recombinant proteins of Escherichia coli, yeast, and mammalian cells using orthogonal pairs of tRNA...

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

mentioning

confidence: 99%

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Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification

Bezerra

Simões

Lee

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

110

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“…Because protein function is dictated by structure and, thus, amino acid sequence, mistakes in translation of the genetic code can yield drastic alterations in the properties of products of mistranslation. Quality control mechanisms exist that help maintain translation fidelity, limiting mistranslation to one mistake in 10 3 -10 4 codons under normal growth conditions (1). The aminoacyl-tRNA synthetase (aaRS) 2 enzymes, which pair amino acids and tRNAs for participation as substrates in protein synthesis, are among the primary determinants of translational fidelity.…”

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“…In the event that a non-cognate amino acid or tRNA is utilized as an aaRS substrate, the resulting mispaired aminoacyl-tRNA (aa-tRNA) species may lead to an error in decoding at the ribosome, resulting in mistranslation of the genetic code. To limit these errors, aaRS enzymes have evolved strict quality control mechanisms, which typically confer high substrate specificity and contribute to an estimated rate of mispaired aatRNA production limited to roughly 1 per 3000 aa-tRNAs produced (2), although deviations exist between species and specific aaRSs (1,3,4). Some aaRS enzymes hydrolyze or selectively release (5) aminoacyl-adenylate (aa-AMP) species resulting from non-cognate amino acid activation in a quality control step before transfer of the aminoacyl moiety to tRNA.…”

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Multiple Quality Control Pathways Limit Non-protein Amino Acid Use by Yeast Cytoplasmic Phenylalanyl-tRNA Synthetase

Moghal

Hwang

Faull

et al. 2016

Journal of Biological Chemistry

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Non-protein amino acids, particularly isomers of the proteinogenic amino acids, present a threat to proteome integrity if they are mistakenly inserted into proteins. Quality control during aminoacyl-tRNA synthesis reduces non-protein amino acid incorporation by both substrate discrimination and proofreading. For example phenylalanyl-tRNA synthetase (PheRS) proofreads the non-protein hydroxylated phenylalanine derivative m-Tyr after its attachment to tRNA Phe . We now show in Saccharomyces cerevisiae that PheRS misacylation of tRNA Phe with the more abundant Phe oxidation product o-Tyr is limited by kinetic discrimination against o-Tyr-AMP in the transfer step followed by o-Tyr-AMP release from the synthetic active site. This selective rejection of a non-protein aminoacyl-adenylate is in addition to known kinetic discrimination against certain noncognates in the activation step as well as catalytic hydrolysis of mispaired aminoacyl-tRNA Phe species. We also report an unexpected resistance to cytotoxicity by a S. cerevisiae mutant with ablated post-transfer editing activity when supplemented with o-Tyr, cognate Phe, or Ala, the latter of which is not a substrate for activation by this enzyme. Our phenotypic, metabolomic, and kinetic analyses indicate at least three modes of discrimination against non-protein amino acids by S. cerevisiae PheRS and support a non-canonical role for SccytoPheRS post-transfer editing in response to amino acid stress.

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Aminoacyl‐ t RNA Synthetases

2007

Hawley's Condensed Chemical Dictionary

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A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans

Abstract: Background: Genetic code alterations have been reported in mitochondrial, prokaryotic, and eukaryotic cytoplasmic translation systems, but their evolution and how organisms cope and survive such dramatic genetic events are not understood.

Cited by 107 publications

References 63 publications

Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification

Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification

Multiple Quality Control Pathways Limit Non-protein Amino Acid Use by Yeast Cytoplasmic Phenylalanyl-tRNA Synthetase

Aminoacyl‐ t RNA Synthetases

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