Genome-wide analysis of the HAK/KUP/KT gene family in Spinacia oleracea L.: Insights into potential stress-related regulatory mechanisms

Abstract

Potassium is an essential macronutrient that contributes to ion homeostasis, protein synthesis, and plant responses to biotic and abiotic stresses. The HAK/KUP/KT gene family plays a key role in regulating potassium uptake and transport in plants. Despite the functional importance of these transporters, this gene family has not yet been comprehensively characterized in Spinacia oleracea. Therefore, this study conducted a genome-wide analysis of HAK/KUP/KT genes in S. oleracea, including chromosomal localization, physicochemical characterization, phylogenetic relationships, gene structure, conserved motifs, secondary and tertiary protein structures, subcellular localization, cis-acting elements, and miRNA target prediction. A total of 32 HAK/KUP/KT genes, designated as SoHAKs, were identified across six chromosomes of S. oleracea. Among these genes, ten were located on chromosome 1, indicating an uneven chromosomal distribution. Phylogenetic analysis classified the SoHAK family into three major groups. Physicochemical characterization revealed that most SoHAK proteins were basic in nature and predicted to be unstable. Structural analyses indicated that most SoHAK proteins contained α-helices, β-strands, and loop regions. Subcellular localization prediction showed that most SoHAK proteins were associated with the plasma membrane, supporting their potential roles in potassium transport. Promoter and miRNA target analyses further suggested that several SoHAK genes may be involved in stress-related regulatory mechanisms. Notably, SoHAK2, SoHAK3, SoHAK4, SoHAK10, SoHAK26, SoHAK27, SoHAK29, SoHAK30, and SoHAK32 emerged as candidate genes for future functional studies. Overall, these findings provide a genomic framework for further investigating the potential roles of HAK/KUP/KT genes in potassium transport and stress-related regulatory mechanisms in S. oleracea.

Keywords

• Abiotic stress
• HAK/KUP/KT gene family
• miRNA
• potassium transport
• Spinacia oleracea

Ispanak (Spinacia oleracea L.) HAK/KUP/KT gen ailesinin genom çapında analizi: Potansiyel strese bağlı düzenleyici mekanizmalara ilişkin öngörüler

Abstract

Potasyum, iyon homeostazının sürdürülmesi, protein sentezi ve bitkilerin biyotik ile abiyotik streslere verdiği yanıtlar açısından temel öneme sahip bir makro besin elementidir. HAK/KUP/KT gen ailesi, bitkilerde potasyum alımı ve taşınmasının düzenlenmesinde kritik rol oynamaktadır. Ancak bu gen ailesi, Spinacia oleracea'da şimdiye kadar kapsamlı olarak karakterize edilmemiştir. Bu nedenle, bu çalışmada S. oleracea'daki HAK/KUP/KT genleri genom çapında analiz edilerek kromozomal lokalizasyon, fizikokimyasal özellikler, filogenetik ilişkiler, gen yapısı, korunmuş motifler, ikincil ve üçüncül protein yapıları, subselüler lokalizasyon, cis-etkili düzenleyici elementler ve miRNA hedef tahminleri incelenmiştir. Analizler sonucunda, S. oleracea'nın altı kromozomu üzerinde yer alan ve SoHAKs olarak adlandırılan toplam 32 HAK/KUP/KT geni belirlenmiştir. Bu genlerin onunun 1. kromozom üzerinde bulunması, kromozomal dağılımın dengesiz olduğunu göstermiştir. Filogenetik analiz, SoHAK gen ailesinin üç ana gruba ayrıldığını ortaya koymuştur. Fizikokimyasal analizler, SoHAK proteinlerinin büyük çoğunluğunun bazik karakterde olduğunu ve kararsız proteinler olarak tahmin edildiğini göstermiştir. Yapısal analizler, çoğu SoHAK proteininin α-heliks, β-tabaka ve döngü bölgelerinden oluştuğunu ortaya koymuştur. Subselüler lokalizasyon tahminleri, SoHAK proteinlerinin büyük ölçüde plazma membranında bulunduğunu ve bunun potasyum taşınmasındaki olası görevlerini desteklediğini göstermiştir. Promotör ve miRNA hedef analizleri ise bazı SoHAK genlerinin strese bağlı düzenleyici mekanizmalarda rol oynayabileceğini ortaya koymuştur. Özellikle SoHAK2, SoHAK3, SoHAK4, SoHAK10, SoHAK26, SoHAK27, SoHAK29, SoHAK30 ve SoHAK32 gelecekte gerçekleştirilecek fonksiyonel çalışmalar için aday genler olarak öne çıkmıştır. Sonuç olarak bu bulgular, S. oleracea'da HAK/KUP/KT genlerinin potasyum taşınması ve strese bağlı düzenleyici mekanizmalardaki potansiyel rollerinin daha ayrıntılı olarak araştırılmasına yönelik önemli bir genomik altyapı sağlamaktadır.

Keywords

• Abiyotik stres
• HAK/KUP/KT gen ailesi
• miRNA
• potasyum taşınımı
• Spinacia oleracea

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