Saccharomyces cerevisiae Genom Seviye Metabolik Modellerinin 20 Yıllık Gelişimi

Abstract

Saccharomyces cerevisiae, hem endüstride büyük değeri olan bir mikroorganizma hem de biyolojik ve tıbbi araştırmalarda temel bir model sistemidir. Önemini artıran bir diğer unsur, genomu tamamen dizilenmiş ilk ökaryot olmasıdır; bu durum hücresel işlev, düzenleme ve metabolizmanın sistematik olarak incelenmesine olanak sağlamıştır. Bu genomik temele dayanarak, araştırmacılar son yirmi yılda en az 16 adet Saccharomyces cerevisiae genom seviye metabolik modeli (GEM) geliştirmiştir. Bu modeller, maya metabolik ağını ve gen–reaksiyon ilişkilerini ortaya koymak için kapsamlı biyokimyasal, genetik ve fizyolojik verileri bütünleştirir. Bu modellerden nicel tahminler elde edebilmek için GEM’ler genellikle akı dengesi analizi (FBA) kullanılarak değerlendirilir. FBA, metabolizmayı stokiyometrik matrisler aracılığıyla temsil eden ve kütle dengesi ile termodinamik kısıtlamalar uygulayan kısıtlara dayalı bir hesaplama yaklaşımıdır. Biyokütle üretimi gibi biyolojik amaçları optimize ederek, detaylı kinetik parametrelere ihtiyaç duymadan gerçekleştirilebilir akı dağılımlarını tahmin eder. GEM ve FBA birlikte, maya metabolizmasının incelenmesinde güçlü bir platform oluşturarak büyüme, gen esansiyelliği, metabolik darboğazlar, teorik verimler ve genetik ya da çevresel değişikliklere verilen tepkiler hakkında geniş ölçekli tahminler yapılmasını mümkün kılar. Bu derlemede, S. cerevisiae’nin genom seviye metabolik modellerinin son yirmi yıldaki başlıca gelişmeleri özetlenmektedir.

Keywords

• Genom seviye metabolik model (GEM)
• Saccharomyces cerevisiae
• Akı denge analizi (FBA)

Two Decades of Genome-Scale Metabolic Modeling for Saccharomyces cerevisiae

Abstract

Saccharomyces cerevisiae (baker’s yeast) is both a highly valuable industrial microorganism and a central model system in biological and medical research. Its importance is strengthened by being the first eukaryote to have its genome fully sequenced and publicly released, providing the basis for systematic studies of cellular function, regulation, and metabolism. Using this genomic foundation, researchers have developed at least 16 genome-scale metabolic models over the past two decades. These reconstructions integrate extensive biochemical, genetic, and physiological data to map the yeast metabolic network and its gene–reaction relationships. Genome scale metabolic models are commonly analyzed using flux balance analysis, a constraint-based computational framework that represents metabolism through stoichiometric matrices and applies mass-balance. By optimizing biological objectives such as biomass production, flux balance analysis predicts feasible flux distributions without requiring detailed kinetic parameters. Together, genome scale metabolic models and flux balance analysis form a powerful platform for studying yeast metabolism, enabling large-scale predictions of growth, gene essentiality, metabolic bottlenecks, theoretical yields, and responses to genetic or environmental changes. This review summarizes key advances in genome-scale metabolic modeling of Saccharomyces cerevisiae over the past twenty three years.

Keywords

• Genome scale metabolic model (GEM)
• Saccharomyces cerevisiae
• Flux balance analysis (FBA)

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