Yüksek Bitki Türlerindeki Sinamil alkol dehidrogenaz (CAD) Proteinlerinin Biyoinformatiksel Analizi

Sinamil alkol dehidrogenaz (CAD) (EC 1.1.1.195) lignin ve lignin üretimindeki öncül çeşitli fenil propenil aldehit türevlerinin indirgenmesinde görev alan bir enzimdir. Türlere özgü olan CAD genleri, son yıllarda önemli derecede tanımlanmıştır. Bu çalışmada CAD genlerinin (enzim veya proteinlerinin) bioinformatik araçlar kullanılarak karakterize edilip, sınıflandırılması amaçlanmıştır. 16 farklı bitki türünden elde edilen CAD nükleotit ve amino asit dizileri fizyolojik özellikler, filogenetik ve korunmuş motif bölgelerinin karşılaştırılması için kullanılmıştır. Bu amaçla CAD proteinlerinin sekans, filojenik ve yapısal analizleri çeşitli sunucular yardımıyla yapılmıştır. Bütün incelenen CAD dizilerinin alkol dehidrogenaz (PF08240) ve çinko bağlayıcı dehidrogenaz domainlerine sahip oldukları gözlenmiştir (PF00107). Fizyokimyasal analiz sonuçlarına göre, CAD’lerin önemli bir kısmının (%81,25’i) asidik karakterde olduğu gözlenmiştir. Bu proteinlerin amino asit uzunlukları (aa) ve moleküler ağırlıklarının (kDa) 356 -367 ve 38,6-40,5 arasında sırasıyla değişmekte olduğu belirlenmiştir. Dizi benzerlikleri en yüksek Sorghum bicolorile Zea mays (%95,3), Panicum virgatum ile Sorghum bicolor (%90,9) ve Oryza sativa ile Zea mays (% 87,1) arasında bulunmuştur. İncelenen CAD genlerinin intron ve ekzon yapıları birbirlerinden farklılık göstermiş olduğu ve ekzon sayılarının iki ve altı arasında değiştiği belirlenmiştir. Çalışmadaki tek çenekli türler olan S. bicolor, P. virgatum, Z. mays, ve O. sativa’nın dört ekzona sahip olduğu; Brachypodium distachyon’un ise sadece iki ekzona sahip olduğu gözlenmiştir. Filogenetik analiz neticesinde CAD proteinlerinin sadece iki ana gruba ayrıldığı saptanmış; en yüksek bootstrap değerleri sırasıyla şu şekilde bulunmuştur: Fragaria vesca-Prunus persica grubu (%100), Glycine max-Medicago truncatula (%81), and S. bicolor-Z. mays (%72). İncelenen CAD’lerin 3 boyutlu analizlerine göre, Oryza ve Vitis CAD’leri, araştırmadaki diğer bitki CAD’lerinden en fazla ayrılma göstermiştir. Son olarak bu çalışmadaki veriler, farklı bitkilerdeki CAD genleri veya proteinlerinin tanımlanması ve değerlendirmesini amaçlayan yeni çalışmalara katkı sağlayacaktır.

Bioinformatical Analyses of cinnamyl alcohol dehydrogenase (CAD) proteins from higher plant species

Cinnamyl alcohol dehydrogenase (CAD) (EC 1.1.1.195) is an enzyme functioning in the reduction of variousphenylpropenyl aldehyde derivatives which are precursors in lignin and lignan production. Species-specific CADgenes have been extensively identified in recent years. In this study, we used bioinformatics tools to characterizeand classify plant CADs. The amino acid and nucleotide sequences of 16 CADs from different plant species wereused to compare their physiological properties, phylogeny, and conserved motifs. For this purpose, sequence,phylogenetical, structural analyses of proteins were conducted using various servers. All plant CADs had thecharacteristic alcohol dehydrogenase (PF08240) and zinc-binding dehydrogenase domains (PF00107). Accordingto the physicochemical analysis, it was revealed that the most of plant CADs (81.25%) were in acidic character.Sequence length (aa) and molecular weight (kDa) of CAD proteins were found in range of 356 -367 and 38.6-40.5respectively. The highest sequence similarities were found between Sorghum bicolor and Zea mays (95.3%),Panicum virgatum and Sorghum bicolor (90.9%), and Oryza sativa and Zea mays (87.1%) respectively. PlantCADs showed divergent exon-intron structures in which exon numbers were ranged from two to six. Four monocotspecies (S. bicolor, P. virgatum, Z. mays, and O. sativa) have four exons, whereas Brachypodium distachyoncontains only two exons. Phylogenetic analysis revealed that the CAD proteins mainly divided into two groups.The highest bootstrap values were found as follows: Fragaria vesca-Prunus persica clade (100%), Glycine maxMedicago truncatula (81%), and S. bicolor-Z. mays (72%). The 3D structures of plant CADs showed that Oryzaand Vitis had the most divergent structures when compared to the other plant species. Eventually, the datarepresented here contribute to studies aiming at evaluating the plant CADs extensively and at identifying new CADgenes in other plants.

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