PvTLP genlerinin genom çaplı tespit ve karakterizasyonu

Year 2022, Issue: 34, 676 - 684, 31.03.2022

Ayşe Gül Kasapoğlu , Ahmed Sidar Aygören , Selman Muslu , Burak Muhammed Öner , Murat Isıyel , Esra Yaprak , Sümeyra Uçar , Recep Aydınyurt , Büşra Uzun , Emre İlhan , Murat Aydın

https://doi.org/10.31590/ejosat.1083519

Cited By: 1

Abstract

TUBBY-like proteinleri (TLP) C terminal bölgede TUB domaini ve ilave olarak N terminal bölgede F-Box domaini içeren çok işlevli bir proteindir. Memelilerde nöronal gelişme ve farklılaşmada rol oynarken bitkilerde strese karşı yanıtta, sinyal iletimi ve hücre döngüsünün kontrolü gibi birçok işleve sahiptir. Bitkiler sesil organizmalar olduğu için çevresel streslerden kaçamazlar. Bu yüzden strese karşı savunma mekanizmalarını aktifleştirmektedirler. Bu savunma mekanizmalarından biri de çeşitli gen ya da gen ailelerinin ifade seviyelerinin artırılması ya da azaltılmasıdır. TLP genleri ilk olarak obez farelerde tanımlanmış olup ardından diğer ökaryotik hücrelerde de tanımlanmaya başlamıştır. Fakat Phaseolus vulgaris genomunda TUBBY-like proteinlerinin karakterizasyonu henüz yapılmamıştır. Bu çalışmanın amacı P. vulgaris genomundaki TLP genlerini tespit ve karakterize ederek çeşitli biyoinformatik araçlarla genom bazında analizini gerçekleştirmektir. P. vulgaris genomunda 10 adet TLP geni belirlenmiştir. PvTLP7 geni hariç diğer PvTLP genleri F-Box domaini içermekte ve tüm PvTLP genleri TUB domainini barındırmaktadır. PvTLP proteinlerinin amino asit sayıları 360-431, moleküler ağırlıkları 40,46-48,12 kDa ve teorik izoelektrik noktası 9,09-9,71 arasında olup PvTLP proteinleri bazik özellik göstermektedir. Arabidopsis thaliana, Glycine max ve P. vulgaris TLP genleri arasındaki filogentik ilişkiler tespit edilmiş olup 3 ana gruba ayrıldığı bulunmuştur. Kuraklık ve tuz stresi altındaki PvTLP genlerinin ifade seviyeleri in siliko olarak incelenmiş olup PvTLP1 ve PvTLP7 genlerinin ifade seviyelerinde farklılıklar gözlemlenmiştir. Bu çalışmadan elde edilen bilgiler ışığında TLP genlerinin fasulyedeki işlevi aydınlatılarak gelecekte yapılacak olan fonksiyonel çalışmalara zemin oluşturacaktır.

Keywords

TUBBY, F-Box, karakterizasyon, filogenetik, sinteni

Genome-wide characterization and identification of PvTLP genes

Abstract

TUBBY-like proteins (TLP) are multifunctional proteins that contain a TUB domain in the C-terminal region and an additional F-Box domain in the N-terminal region. While it plays a role in neuronal development and differentiation in mammals, it has many functions such as the response to stress, signal transduction and cell cycle control in plants. Since plants are sessile organisms, they cannot escape from environmental stresses. Therefore, they activate their defense mechanisms against stress. One of these defense mechanisms is to increase or decrease the expression levels of various genes or gene families. TLP genes were first identified in obese mice and then began to be expressed in other eukaryotic cells. However, characterization of TUBBY-like proteins in the Phaseolus vulgaris genome has not yet been performed. The purpose of this study is to detect and recognize TLP genes in the P. vulgaris genome, as well as to analyze them using various bioinformatics tools across the genome. Ten TLP genes were identified in the P. vulgaris genome. Except for the PvTLP7 gene, other PvTLP genes contain the F-Box domain and all PvTLP genes contain the TUB domain. PvTLP proteins have an amino acid number of 360-431, a molecular weight of 40.46-48.12 kDa, and a theoretical isoelectric point of 9.09-9.71, and PvTLP proteins show basic properties. Phylogenetic relationships between Arabidopsis thaliana, Glycine max and P. vulgaris TLP genes were determined and they were found to be divided into 3 main groups. Expression levels of PvTLP genes under drought and salt stress were examined in silico, and differences in expression levels of PvTLP1 and PvTLP7 genes were observed. In the light of the information obtained from this study, the function of TLP genes in beans will be clarified and will form the basis for future functional studies.

Keywords

TUBBY, F-Box, characterization, phylogenetic, synteny

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