Ser or Leu: structural snapshots of mistranslation in Candida albicans

A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans

Candida albicans is a diploid pathogen known for its ability to live as a commensal fungus in healthy individuals but causing both superficial infections and disseminated candidiasis in immunocompromised patients where it is associated with high morbidity and mortality. Its success in colonizing the human host is attributed to a wide range of virulence traits that modulate interactions between the host and the pathogen, such as optimal growth rate at 37 °C, the ability to switch between yeast and hyphal forms, and a remarkable genomic and phenotypic plasticity. A fascinating aspect of its biology is a prominent heterogeneous proteome that arises from frequent genomic rearrangements, high allelic variation, and high levels of amino acid misincorporations in proteins. This leads to increased morphological and physiological phenotypic diversity of high adaptive potential, but the scope of such protein mistranslation is poorly understood due to technical difficulties in detecting and quantifying amino acid misincorporation events in complex protein samples. We have developed and optimized mass spectrometry and bioinformatics pipelines capable of identifying rare amino acid misincorporation events at the proteome level. We have also analyzed the proteomic profile of an engineered C. albicans strain that exhibits high level of leucine misincorporation at protein CUG sites and employed an in vivo quantitative gain-of-function fluorescence reporter system to validate our LC-MS/MS data. C. albicans misincorporates amino acids above the background level at protein sites of diverse codons, particularly at CUG, confirming our previous data on the quantification of leucine incorporation at single CUG sites of recombinant reporter proteins, but increasing misincorporation of Leucine at these sites does not alter the translational fidelity of the other codons. These findings indicate that the C. albicans statistical proteome exceeds prior estimates, suggesting that its highly plastic phenome may also be modulated by environmental factors due to translational ambiguity.

Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess

Comprehensive whole genome sequencing (WGS) with hybrid assembly of a multi-drug resistant (MDR) Candida albicans (CA) isolate causing cerebral abscess was performed using Illumina paired end and Oxford Nanopore long read technologies. The innovative technologies utilized here enabled us to resolve fragmented assemblies, and implement comprehensive and detailed genomic analyses involved in antifungal resistance of Candida spp. Functionally important genes (MDR1, CDR2 and SQN2) involved in antifungal resistance were identified and a phylogenetic analysis of the clinical isolate was performed. Additionally, our clinical isolate was found to share 4 single nucleotide polymorphisms with two other sequenced strains of MDR C. auris (381 and 386) including translation elongation factor EF1α and EF3, ATPase activity associated proteins, and the lysine tRNA ligase.

Bacterial translation machinery for deliberate mistranslation of the genetic code

Inaccurate expression of the genetic code, also known as mistranslation, is an emerging paradigm in microbial studies. Growing evidence suggests that many microbial pathogens can deliberately mistranslate their genetic code to help invade a host or evade host immune responses. However, discovering different capacities for deliberate mistranslation remains a challenge because each group of pathogens typically employs a unique mistranslation mechanism. In this study, we address this problem by studying duplicated genes of aminoacyl-transfer RNA (tRNA) synthetases. Using bacterial prolyl-tRNA synthetase (ProRS) genes as an example, we identify an anomalous ProRS isoform, ProRSx, and a corresponding tRNA, tRNA^ProA, that are predominately found in plant pathogens from Streptomyces species. We then show that tRNA^ProA has an unusual hybrid structure that allows this tRNA to mistranslate alanine codons as proline. Finally, we provide biochemical, genetic, and mass spectrometric evidence that cells which express ProRSx and tRNA^ProA can translate GCU alanine codons as both alanine and proline. This dual use of alanine codons creates a hidden proteome diversity due to stochastic Ala→Pro mutations in protein sequences. Thus, we show that important plant pathogens are equipped with a tool to alter the identity of their sense codons. This finding reveals the initial example of a natural tRNA synthetase/tRNA pair for dedicated mistranslation of sense codons.

Translational quality control and reprogramming during stress adaptation

Organisms encounter stress throughout their lives, and therefore require the ability to respond rapidly to environmental changes. Although transcriptional responses are crucial for controlling changes in gene expression, regulation at the translational level often allows for a faster response at the protein levels which permits immediate adaptation. The fidelity and robustness of protein synthesis are actively regulated under stress. For example, mistranslation can be beneficial to cells upon environmental changes and also alters cellular stress responses. Additionally, stress modulates both global and selective translational regulation through mechanisms including the change of aminoacyl-tRNA activity, tRNA pool reprogramming and ribosome heterogeneity. In this review, we draw on studies from both the prokaryotic and eukaryotic systems to discuss current findings of cellular adaptation at the level of translation, specifically translational fidelity and activity changes in response to a wide array of environmental stressors including oxidative stress, nutrient depletion, temperature variation, antibiotics and host colonization.

Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions

Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that play a fundamental role in protein synthesis. They catalyze the esterification of specific amino acids to the 3'-end of their cognate tRNAs and therefore play a pivotal role in protein synthesis. Although previous studies suggest that aaRS-dependent errors in protein synthesis can be beneficial to some microbial species, evidence that reduced aaRS fidelity can be adaptive is limited. Using bioinformatics analyses, we identified two distinct leucyl-tRNA synthetase (LeuRS) genes within all genomes of the archaeal family Sulfolobaceae. Remarkably, one copy, designated LeuRS-I, had key amino acid substitutions within its editing domain that would be expected to disrupt hydrolytic editing of mischarged tRNA^Leu and to result in variation within the proteome of these extremophiles. We found that another copy, LeuRS-F, contains canonical active sites for aminoacylation and editing. Biochemical and genetic analyses of the paralogs within Sulfolobus islandicus supported the hypothesis that LeuRS-F, but not LeuRS-I, functions as an essential tRNA synthetase that accurately charges leucine to tRNA^Leu for protein translation. Although LeuRS-I was not essential, its expression clearly supported optimal S. islandicus growth. We conclude that LeuRS-I may have evolved to confer a selective advantage under the extreme and fluctuating environmental conditions characteristic of the volcanic hot springs in which these archaeal extremophiles reside.

Genetic code ambiguity modulates the activity of a C. albicans MAP kinase linked to cell wall remodeling

The human fungal pathogen Candida albicans ambiguously decodes the universal leucine CUG codon predominantly as serine but also as leucine. C. albicans has a high capacity to survive and proliferate in adverse environments but the rate of leucine incorporation fluctuates in response to different stress conditions. C. albicans is adapted to tolerate this ambiguous translation through a mechanism that combines drastic decrease in CUG usage and reduction of CUG-encoded residues in conserved positions in the protein sequences. However, in a few proteins, the residues encoded by CUG codons are found in strictly conserved positions, suggesting that this genetic code alteration might have a functional impact. One such example is Cek1, a central signaling protein kinase that contains a single CUG-encoded residue at a conserved position, whose identity might regulate the correct flow of information across the MAPK cascade. Here we show that insertion of a leucine at the CUG-encoded position decreases the stability of Cek1, apparently without major structural alterations. In contrast, incorporation of a serine residue at the CUG position induces the autophosphorylation of the conserved tyrosine residue of the Cek1 ²³¹TEY²³³ motif, and increases its intrinsic kinase activity in vitro. These findings show that CUG ambiguity modulates the activity of Cek1, a key kinase directly linked to morphogenesis and virulence in C. albicans.

Translational fidelity and mistranslation in the cellular response to stress

Faithful translation of mRNA into the corresponding polypeptide is a complex multistep process, requiring accurate amino acid selection, transfer RNA (tRNA) charging and mRNA decoding on the ribosome. Key players in this process are aminoacyl-tRNA synthetases (aaRSs), which not only catalyse the attachment of cognate amino acids to their respective tRNAs, but also selectively hydrolyse incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. This aaRS proofreading provides quality control checkpoints that exclude non-cognate amino acids during translation, and in so doing helps to prevent the formation of an aberrant proteome. However, despite the intrinsic need for high accuracy during translation, and the widespread evolutionary conservation of aaRS proofreading pathways, requirements for translation quality control vary depending on cellular physiology and changes in growth conditions, and translation errors are not always detrimental. Recent work has demonstrated that mistranslation can also be beneficial to cells, and some organisms have selected for a higher degree of mistranslation than others. The aims of this Review Article are to summarize the known mechanisms of protein translational fidelity and explore the diversity and impact of mistranslation events as a potentially beneficial response to environmental and cellular stress.

Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair

Fidelity of translation, which is predominately dictated by the accuracy of aminoacyl-tRNA synthetases in pairing amino acids with correct tRNAs, is of central importance in biology. Yet, deliberate modifications of translational fidelity can be beneficial. Here we found human and not E. coli AlaRS has an intrinsic capacity for mispairing alanine onto nonalanyl-tRNAs including tRNA^Cys. Consistently, a cysteine-to-alanine substitution was found in a reporter protein expressed in human cells. All human AlaRS-mischarged tRNAs have a G4:U69 base pair in the acceptor stem. The base pair is required for the mischarging. By solving the crystal structure of human AlaRS and comparing it to that of E. coli AlaRS, we identified a key sequence divergence between eukaryotes and bacteria that influences mischarging. Thus, the expanded tRNA specificity of AlaRS appears to be an evolutionary gain-of-function to provide posttranscriptional alanine substitutions in eukaryotic proteins for potential regulations.

Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis

Translation of genetic information into functional proteins is critical for all cellular life. Accurate protein synthesis relies on proper aminoacylation of transfer RNAs (tRNAs) and decoding of mRNAs by the ribosome with the use of aminoacyl-tRNAs. Mistranslation can lead to pathologic consequences. All cells contain elaborate quality control mechanisms in translation, although translational fidelity may be regulated by various factors such as nutrient limitation or reactive oxygen species. Translation fidelity is maintained via the accuracy of tRNA aminoacylation by the aminoacyl-tRNA synthetases and matching of the mRNA codon with the tRNA anticodon by the ribosome. Stringent substrate discrimination and proofreading are critical in aminoacylating tRNAs with their cognate amino acid to maintain high accuracy of translation. Although the composition of the cellular proteome generally adheres to the genetic code, accumulating evidence indicates that cells can also deliberately mistranslate; they synthesize mutant proteins that deviate from the genetic code in response to stress or environmental changes. Mistranslation with tRNA charged with noncognate amino acids can expand the proteome to enhance stress response and help adaptation. Here, we review current knowledge on mistranslation through tRNA misacylation and describe advances in our understanding of translational control in the regulation of stress response and human diseases.