YARS2 Human

What is YARS2 and what is its primary function in human mitochondria?

YARS2 encodes mitochondrial tyrosyl-tRNA synthetase, an essential enzyme that specifically aminoacylates tyrosine to mitochondrial tRNATyr (mt-tRNATyr) . This aminoacylation process is a crucial step in mitochondrial protein synthesis, as it ensures the correct incorporation of tyrosine residues into nascent peptide chains during mitochondrial translation. The process occurs in two sequential steps: first, the enzyme activates tyrosine with ATP to form tyrosyl-AMP, then transfers the activated tyrosine to the 3' end of mt-tRNATyr.

The YARS2 protein functions within the mitochondrial matrix as an obligate dimer. Each charged tRNA subsequently delivers tyrosine to the mitochondrial ribosome during protein synthesis, enabling the translation of the 13 proteins encoded by mitochondrial DNA. These proteins are essential components of the respiratory chain complexes that drive oxidative phosphorylation.

Functional YARS2 is therefore critical for mitochondrial energy production, explaining why pathogenic variants in this gene often manifest as mitochondrial disease with prominent myopathy, lactic acidosis, and frequently sideroblastic anemia. The gene's involvement in fundamental mitochondrial processes also explains why severe variants can be associated with neonatal fatality, as documented in cases of compound heterozygous mutations .

What are the key clinical manifestations of YARS2-related mitochondrial disease?

YARS2-related mitochondrial disease presents with a constellation of clinical features, primarily characterized as myopathy, lactic acidosis, and sideroblastic anemia (MLASA2). According to a comprehensive study of 17 patients with YARS2 variants, the predominant clinical manifestations include:

• Myopathy: Observed in 88% of patients, presenting as generalized muscle weakness, often with reduced muscle strength (ranging from 3/5 to 4/5) .

• Lactic acidosis: Elevated blood lactate levels were identified in 88% of individuals .

• Sideroblastic anemia: Present in 71% of patients, though not all required transfusions .

• Cardiomyopathy: Hypertrophic cardiomyopathy was observed in 53% of patients, with some experiencing high-output cardiac failure or progressing to end-stage cardiac failure .

• Respiratory insufficiency: Observed in 47% of patients, ranging from restrictive patterns to more severe presentations requiring non-invasive ventilation (NIV) .

The clinical presentation varies significantly between patients. The median age at onset was 1.5 years (interquartile range [IQR] 9.8 years), with a range from 1 week to 31 years. Most patients (82%) presented within the first decade of life, while some presented in adolescence or adulthood . The disease can be fatal, with 35% of patients in the studied cohort succumbing to the disease at a median age of 25.5 years .

Central nervous system involvement appears to be rare in YARS2-related mitochondrial disease, distinguishing it from some other mitochondrial disorders. Additional features observed in some patients include facial weakness and scapular winging . The table below summarizes clinical characteristics of selected patients with YARS2 variants:

a Deceased; NIV = non-invasive ventilation; NA = not available

How are YARS2 variants identified and classified in clinical research?

YARS2 variants are identified and classified through a multi-step process combining genetic analysis, clinical correlation, and functional studies. Initially, variants are detected through next-generation sequencing approaches, including targeted gene panels for mitochondrial diseases, whole exome sequencing, or whole genome sequencing. These methods identify potential pathogenic variants in the YARS2 gene.

Variants are classified according to standard guidelines based on several criteria including frequency in population databases, in silico prediction of pathogenicity, conservation of affected residues across species, previous reports in patients with similar phenotypes, and segregation in affected families. For novel or variants of uncertain significance, functional validation becomes essential.

Yeast modeling serves as a valuable approach for functional validation. Human YARS2 is highly conserved in phylogenesis, including in yeast. For conserved residues (like Leu392, which corresponds to Leu411 in yeast), mutant alleles are generated directly. For non-conserved residues (like Cys369, which is Leu391 in yeast), researchers create "humanized" versions by mutating the yeast sequence to match human wild-type before introducing the variant for testing . Oxidative growth and respiration measurements evaluate the impact of YARS2 variants on mitochondrial function in these yeast models .

Muscle biopsy analysis provides additional evidence through histochemical evaluation for mitochondrial dysfunction, such as global cytochrome-c oxidase (COX) deficiency, presence of ragged red fibers (RRFs), and respiratory chain complex activity measurements, which typically show combined defects involving complexes I, III, and/or IV .

Researchers also correlate specific YARS2 variants with clinical presentations to establish genotype-phenotype patterns. For example, microsatellite genotyping has demonstrated founder effects for certain variants, such as the p.Leu392Ser variant identified in Scottish patients .

Through these comprehensive approaches, researchers can establish the pathogenicity of YARS2 variants and expand understanding of the genotype-phenotype spectrum associated with this gene.

What is the genetic inheritance pattern of YARS2-related diseases?

YARS2-related mitochondrial disease follows an autosomal recessive inheritance pattern. Affected individuals typically inherit two pathogenic variants in the YARS2 gene, one from each parent. Several genetic scenarios can occur in this inheritance pattern:

Homozygous variants occur when patients inherit the same pathogenic variant from both parents, which is more common in consanguineous families. In the reported cohort, at least one patient of Scottish ethnicity was noted to have consanguineous parents . This pattern typically occurs when both parents carry the same pathogenic variant, often due to shared ancestry.

Compound heterozygous variants are common in YARS2-related disease, where patients inherit two different pathogenic variants, one from each parent. This pattern is particularly significant as recent research has demonstrated that compound heterozygous variants can have synergistic negative effects on enzyme function beyond what would be predicted from each variant individually . The search results specifically mention a study identifying "a pair of compound heterozygous variants in YARS2 that is associated with neonatal fatality" , representing the severe end of the disease spectrum.

Founder effects have also been documented in YARS2-related disease. Microsatellite genotyping demonstrated a common founder effect shared between Scottish patients with the p.Leu392Ser variant, indicating that certain variants may be more prevalent in specific populations due to ancestral mutations . This finding has important implications for genetic screening approaches in populations with known founder mutations.

Carrier parents (those with one pathogenic variant) typically do not show symptoms of the disease due to the recessive inheritance pattern. Each child of carrier parents has a 25% chance of inheriting both pathogenic variants and developing the disease, a 50% chance of being an asymptomatic carrier like the parents, and a 25% chance of inheriting neither variant. This information is crucial for genetic counseling and family planning for those affected by YARS2-related mitochondrial disease.

How does YARS2 function within the mitochondrial translation system?

YARS2 plays a critical role within the mitochondrial translation system, which is essential for the synthesis of proteins encoded by the mitochondrial genome. The primary biochemical function of YARS2 is to catalyze the attachment of tyrosine to its cognate mitochondrial tRNA (mt-tRNATyr). This two-step reaction involves activation of tyrosine with ATP to form tyrosyl-adenylate, followed by transfer of the activated tyrosine to the 3' end of mt-tRNATyr.

Within the mitochondrial translation process, the charged mt-tRNATyr (Tyr-mt-tRNATyr) delivers tyrosine to the mitochondrial ribosome during protein synthesis. This process is essential for accurate translation of all 13 mitochondrially-encoded proteins, which are core components of the respiratory chain complexes. YARS2 functions as an obligate dimer, with each monomer contributing to the enzyme's function. This structural characteristic is particularly relevant when considering the effects of compound heterozygous variants, where the resulting enzyme may contain two different mutant monomers .

Proper YARS2 function directly impacts the integrity of the mitochondrial respiratory chain. Muscle studies in patients with YARS2 variants consistently show global cytochrome-c oxidase deficiency and severe, combined respiratory chain complex activity deficiencies, particularly affecting complexes I, III, and IV . Through its role in mitochondrial translation, YARS2 affects oxidative phosphorylation and ATP synthesis. In knockdown experiments of YARS2 in cancer cell lines, researchers observed decreased steady-state levels of tRNATyr, reduced oxygen consumption rate (OCR), and diminished ATP synthesis .

YARS2 deficiency appears to affect cellular redox status, with knockdown of YARS2 associated with increased reactive oxygen species (ROS) levels . This suggests a role in maintaining mitochondrial redox homeostasis, either directly or indirectly through its impact on respiratory chain function.

Understanding the precise function of YARS2 within the mitochondrial translation system provides insights into the molecular pathogenesis of YARS2-related disease and offers potential targets for therapeutic intervention.

What experimental models are most effective for studying YARS2 mutations?

Multiple experimental models have been employed to study YARS2 mutations, each offering distinct advantages for investigating different aspects of YARS2 function and pathogenicity. The selection of an appropriate model depends on the specific research question and the particular aspect of YARS2 function being investigated.

Yeast models provide an excellent system due to the high conservation of YARS2 throughout phylogenesis. The search results describe detailed yeast modeling approaches for studying YARS2 variants . For conserved residues (e.g., human Leu392 corresponding to yeast Leu411), mutant alleles can be generated directly in the yeast MSY1 gene (the yeast ortholog of YARS2). For non-conserved residues (e.g., human Cys369 corresponding to yeast Leu391), researchers create "humanized" versions by first modifying the yeast residue to match the human wild-type before introducing the variant of interest. Functional assessments include measuring oxidative growth and mitochondrial respiration, which closely correlate with the severity of clinical phenotypes observed in patients .

Patient-derived fibroblasts and myoblasts allow for the study of YARS2 variants in their native genetic context. Immunoblotting from these cells provides insights into YARS2 protein levels and the effects on respiratory chain complex assembly and activity. The search results mention that "Immunoblotting from fibroblasts and myoblasts of an affected Scottish patient showed normal YARS2 protein levels and mild respiratory chain complex defects" , highlighting how these models can reveal unexpected aspects of pathogenesis.

Cancer cell lines with YARS2 knockdown have been used to study both cancer-related and basic functions of YARS2. The search results describe using the human colon cancer cell line SW620 with YARS2 knockdown . This model demonstrated that YARS2 knockdown leads to inhibition of cell proliferation and migration, decreased steady-state levels of tRNATyr, reduced oxygen consumption rate (OCR) and ATP synthesis, increased reactive oxygen species (ROS) levels, and enhanced sensitivity to 5-FU treatment .

Biochemical reconstitution of YARS2 dimers allows for precise biochemical characterization of enzyme activity when different mutations are present in each monomer of the obligate dimer. The search results describe a kinetic model for studying compound heterozygous variants in YARS2 . This model accurately recapitulates disease severity by showing that "while each mutation causes a minor-to-modest defect in aminoacylation in the homodimer of mt-TyrRS, the two mutations in trans synergistically reduce the enzyme activity to a greater effect" .

Each model system offers unique advantages, and the most comprehensive understanding comes from integrating data across multiple model systems to provide a complete picture of YARS2 function and dysfunction.

How do compound heterozygous variants in YARS2 affect enzyme function?

Compound heterozygous variants in YARS2 present a unique analytical challenge due to the dimeric nature of the enzyme. Recent research has provided significant insights into how these variants interact to affect enzyme function. The search results describe a kinetic model that demonstrates how compound heterozygous variants can produce synergistic negative effects on enzyme activity .

YARS2 functions as an obligate dimer, meaning that in patients with compound heterozygous variants, three different dimer configurations can theoretically form: two homodimers (each containing identical mutant monomers) and heterodimers (containing two different mutant monomers). The kinetic model described in the search results specifically addresses "compound heterozygous variants in an obligate enzyme dimer that contains one mutation in one monomer and the other mutation in the second monomer" .

The study found that "while each mutation causes a minor-to-modest defect in aminoacylation in the homodimer of mt-TyrRS, the two mutations in trans synergistically reduce the enzyme activity to a greater effect" . This synergistic reduction in enzyme activity explains why some compound heterozygous combinations can result in severe clinical presentations, including neonatal fatality, even when each variant individually causes only mild dysfunction.

The kinetic model "accurately recapitulates the disease severity" , providing a molecular explanation for the clinical variability observed in patients with different combinations of YARS2 variants. This relationship is particularly important given that previous studies of mitochondrial aminoacyl-tRNA synthetases had shown "limited correlation between disease severity and enzyme activity" .

The research suggests that this kinetic model has "potential for generalization to other diseases with compound heterozygous mutations" , indicating that similar synergistic effects might occur in other dimeric or multimeric proteins involved in human disease. This sophisticated understanding of how compound heterozygous variants interact in YARS2 represents an important advance in mitochondrial disease research. It explains why simple genotype-phenotype correlations may fail when considering each variant in isolation and highlights the importance of functional studies that evaluate the combined effect of variants as they would occur in patients.

What is the relationship between YARS2 variants and disease severity?

The relationship between YARS2 variants and disease severity is complex and multifaceted, influenced by several factors that researchers must consider when evaluating genotype-phenotype correlations. Different YARS2 variants have varying impacts on enzyme function, ranging from mild to severe. Yeast modeling studies have shown that the functional consequences of YARS2 variants "closely correlated with the severity of clinical phenotypes" , suggesting that the degree of enzyme dysfunction is a primary determinant of disease severity.

Compound heterozygosity effects play a crucial role in determining disease severity. As discussed previously, compound heterozygous variants can interact synergistically to produce more severe phenotypes than would be predicted from each variant in isolation. The search results describe a pair of compound heterozygous variants associated with neonatal fatality, representing the most severe end of the disease spectrum . The kinetic model developed for compound heterozygous variants demonstrated that "the two mutations in trans synergistically reduce the enzyme activity to a greater effect" , providing a mechanistic explanation for severe presentations in some compound heterozygous patients.

The clinical presentation of YARS2-related disease ranges from mild, late-onset myopathy to severe, early-onset multisystem disease. In the cohort described in the search results, the median age at onset was 1.5 years (range: 1 week to 31 years), with most patients (82%) presenting within the first decade of life . Mortality was reported in 35% of patients, with a median age of death of 25.5 years , indicating significant variability in disease progression and outcome.

Not all patients with YARS2 variants develop the complete MLASA syndrome. While 88% of patients exhibited myopathy and elevated lactate levels, only 71% manifested with sideroblastic anemia . Additional features like cardiomyopathy (53%) and respiratory insufficiency (47%) were present in approximately half of the patients . Central nervous system involvement was rare, distinguishing YARS2-related disease from some other mitochondrial disorders .

Muscle biopsies from patients with YARS2 variants consistently show global cytochrome-c oxidase deficiency and severe, combined respiratory chain complex activity deficiencies . The specific pattern and severity of respiratory chain defects may correlate with clinical manifestations and disease progression.

Understanding these complex relationships is critical for providing accurate prognostic information to patients and families and for developing targeted therapeutic approaches. The research suggests that comprehensive assessment, including genetic, biochemical, and clinical evaluations, is necessary for accurate prediction of disease course in patients with YARS2 variants.

How does YARS2 expression differ in cancerous versus normal tissues?

Recent research has uncovered an unexpected role for YARS2 in cancer biology, with significant differences in expression between cancerous and normal tissues. The search results report that "the mRNA expression level of YARS2 in colorectal cancer tissues was significantly higher than those in normal intestinal tissues" as determined by quantitative RT-PCR . This finding suggests that YARS2 upregulation may contribute to colorectal cancer pathogenesis or progression.

The functional significance of elevated YARS2 expression in cancer cells has been investigated through knockdown studies. When YARS2 was knocked down in the human colon cancer cell line SW620, researchers observed significant inhibition of cell proliferation, reduced cell migration, decreased steady-state level of tRNATyr, reduced oxygen consumption rate (OCR), diminished ATP synthesis, increased reactive oxygen species (ROS) levels, and enhanced sensitivity to 5-fluorouracil (5-FU) treatment .

Based on these findings, the researchers concluded that "YARS2 might be a carcinogenesis candidate gene and can serve as a potential target for clinical therapy" . The enhanced sensitivity to 5-FU treatment in YARS2 knockdown cells suggests potential applications in combination therapy approaches for colorectal cancer treatment.

The data suggests that YARS2 may support cancer cell growth and survival by maintaining efficient mitochondrial translation, which is necessary for sustaining adequate ATP production through oxidative phosphorylation, managing reactive oxygen species levels, and supporting cancer cell metabolism and proliferation. This role aligns with the growing recognition of mitochondrial function as a critical factor in cancer cell metabolism and survival.

This emerging role of YARS2 in cancer biology represents a surprising connection between a gene previously associated primarily with inherited mitochondrial disease and the somatic alterations underlying cancer progression. It highlights the multifaceted roles of mitochondrial translation factors and suggests that targeting mitochondrial protein synthesis might offer novel therapeutic approaches for certain cancers.

Further research is needed to determine whether YARS2 overexpression is a common feature across other cancer types and to elucidate the exact mechanisms by which YARS2 contributes to cancer cell proliferation and survival.

What mechanisms underlie the tissue-specific effects of YARS2 mutations?

The tissue-specific effects of YARS2 mutations—primarily affecting muscle, blood, and cardiac tissue—represent a puzzling aspect of YARS2-related disease that requires mechanistic investigation. Several factors likely contribute to this tissue specificity, providing important insights for researchers investigating mitochondrial diseases.

Differential energy requirements play a significant role in tissue vulnerability. Tissues most affected by YARS2 mutations (muscle, cardiac tissue, bone marrow) have high energy demands and rely heavily on oxidative phosphorylation. Muscle fibers, particularly type I oxidative fibers, are especially dependent on mitochondrial function, explaining the prominence of myopathy in YARS2-related disease. The search results indicate that 88% of patients with YARS2 variants exhibited myopathy, highlighting the susceptibility of muscle tissue .

Tissue-specific mitochondrial translation regulation may also contribute to differential effects. Different tissues may have varying requirements for specific mitochondrial translation components, including mt-tRNATyr and YARS2. Tissue-specific regulatory factors might influence the expression or function of YARS2 in different cell types. The balance between nuclear and mitochondrial translation may vary across tissues, affecting vulnerability to YARS2 dysfunction.

Variable threshold effects likely explain some of the clinical heterogeneity. Different tissues may have different thresholds for manifestation of mitochondrial dysfunction. The search results show that while 88% of patients exhibited elevated lactate levels and myopathy, only 71% manifested with sideroblastic anemia , suggesting different sensitivity thresholds across tissues.

Compensatory mechanisms may protect certain tissues. Central nervous system involvement was reported as rare in YARS2-related disease , possibly due to compensatory mechanisms specific to neural tissues. These protective mechanisms could include alternative metabolic pathways, differential expression of stress response genes, or tissue-specific mitochondrial dynamics.

YARS2 may interact with tissue-specific proteins or regulatory factors that modulate its function or the consequences of its dysfunction. Such interactions could explain why cardiomyopathy was observed in only 53% of patients and respiratory insufficiency in 47% . Developmental considerations must also be taken into account, as the timing of highest metabolic demand during development differs across tissues. The variable age of onset (from 1 week to 31 years) suggests that developmental factors and age-related changes in tissue-specific energy requirements may influence disease manifestation.

Understanding these tissue-specific mechanisms is crucial for developing targeted therapeutic approaches. Future research might focus on identifying the specific factors that render certain tissues more vulnerable to YARS2 dysfunction while others remain relatively protected, potentially revealing novel therapeutic targets or strategies.

How do YARS2 mutations impact mitochondrial respiratory chain complex activities?

YARS2 mutations have profound and characteristic effects on mitochondrial respiratory chain complex activities, which can be detected through specific biochemical analyses. Muscle studies in patients with YARS2 variants consistently show "global cytochrome-c oxidase deficiency in all patients tested" . Beyond this, patients exhibit "severe, combined respiratory chain complex activity deficiencies" .

The specific pattern typically involves deficiencies in Complex I (NADH:ubiquinone oxidoreductase), Complex III (ubiquinol:cytochrome c oxidoreductase) in some cases, and Complex IV (cytochrome c oxidase) . This pattern is consistent with a global defect in mitochondrial translation, as these complexes contain multiple mitochondrially-encoded subunits. The deficiencies result from impaired aminoacylation of mitochondrial tRNATyr due to YARS2 mutations, reducing the availability of charged tRNATyr for mitochondrial protein synthesis.

This deficiency affects the translation of all 13 mitochondrially-encoded proteins, which are core components of respiratory chain complexes I, III, IV, and V. The degree of impairment in respiratory chain complex activities likely correlates with the severity of the aminoacylation defect caused by specific YARS2 variants.

The combined respiratory chain deficiencies result in impaired electron transport, reduced proton pumping across the inner mitochondrial membrane, decreased ATP synthesis, and increased production of reactive oxygen species. These effects manifest clinically as lactic acidosis (present in 88% of patients) , reflecting the shift from oxidative phosphorylation to glycolysis for ATP production.

While the biochemical defect is presumably present in all tissues, the consequences are most apparent in tissues with high energy demands. In muscle, the respiratory chain deficiencies manifest as myopathy, present in 88% of patients . In the heart, they can lead to hypertrophic cardiomyopathy, observed in 53% of patients . In bone marrow, they contribute to sideroblastic anemia through mechanisms that may involve both impaired heme synthesis and increased ROS production.

Experimental evidence from cancer cell models supports these observations. Knockdown of YARS2 in the SW620 colon cancer cell line resulted in decreased steady-state level of tRNATyr, reduced oxygen consumption rate (OCR), and diminished ATP synthesis . These findings parallel the mitochondrial dysfunction observed in patients with inherited YARS2 mutations.

The direct link between YARS2 mutations and respiratory chain complex deficiencies explains many of the clinical features of YARS2-related disease and provides rationales for potential therapeutic approaches aimed at improving mitochondrial function or bypassing specific bioenergetic defects.

What are the current approaches for functional validation of novel YARS2 variants?

Functional validation of novel YARS2 variants is essential for confirming pathogenicity and understanding disease mechanisms. The search results highlight several complementary approaches that researchers can employ to thoroughly characterize these variants.

Yeast modeling provides a valuable system for evaluating YARS2 variants . Human YARS2 is highly conserved in phylogenesis, including yeast. When the residue of interest is conserved (e.g., human Leu392 corresponds to yeast Leu411), researchers directly create the equivalent mutation in the yeast MSY1 gene. When the residue is not conserved (e.g., human Cys369 corresponds to yeast Leu391), researchers first create a "humanized" version by replacing the yeast residue with the human wild-type amino acid, then introduce the variant of interest. Functional assessment includes oxidative growth measurements and mitochondrial respiration analysis. This approach has demonstrated that yeast modeling "closely correlated with the severity of clinical phenotypes" , validating its utility for predicting pathogenicity.

Patient-derived cell studies offer insights into the effects of variants in their native genetic context. Fibroblasts and myoblasts from patients can be analyzed to assess YARS2 protein levels by immunoblotting and respiratory chain complex assembly and activity. The search results mention that "Immunoblotting from fibroblasts and myoblasts of an affected Scottish patient showed normal YARS2 protein levels and mild respiratory chain complex defects" , highlighting that protein stability may not always be affected despite functional deficits.

Biochemical enzyme assays provide direct measurement of aminoacylation activity using recombinant mutant YARS2 proteins. The search results describe a kinetic model specifically designed for compound heterozygous variants that allows assessment of individual variant effects in homodimers and combined effects in heterodimers containing two different mutant monomers . This approach revealed that "while each mutation causes a minor-to-modest defect in aminoacylation in the homodimer of mt-TyrRS, the two mutations in trans synergistically reduce the enzyme activity to a greater effect" .

Cellular models with YARS2 knockdown or specific mutations can be used to assess steady-state levels of tRNATyr, oxygen consumption rate (OCR), ATP synthesis, and reactive oxygen species (ROS) levels . These approaches provide functional insights into the consequences of YARS2 deficiency or dysfunction.

Integrating multiple approaches provides the most comprehensive evaluation of variant pathogenicity. Correlation with clinical phenotypes helps validate the predictive value of functional studies. The search results emphasize that the kinetic model for compound heterozygous variants "accurately recapitulates the disease severity" , demonstrating the importance of choosing appropriate functional assays for variant characterization.

These functional validation approaches are essential for accurate classification of YARS2 variants, particularly novel or rare variants with uncertain significance based on genetic evidence alone.