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Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods

Year 2021, Volume: 21 Issue: 3, 277 - 294, 31.12.2021

Yusuf Ceylan , Kevser Betül Ceylan Yasemin Çelik Altunoğlu Mehmet Cengiz Baloğlu

https://doi.org/10.17475/kastorman.1049963
Cited By: 1

Abstract

Aim of study: It was aimed to identify and characterize Hsp genes in jujube genome using genomics methods.
Material and method: Protein sequences of jujube Hsp genes were obtained from NCBI databases. GSDS program was used to detect of exon-intron sites. To define the conserved motifs and estimated 3D-structures, Hsp proteins were used in the MEME-SUITE and PHYRE2 program, respectively. miRNAs targeting ZjuHsp transcripts were identified using the psRNATarget Server database. The gene annotations of Hsp proteins were presented by Blast2GO program. Sequence alignment was performed with ClustalW software, and then the phylogenetic tree was drawn using MEGAX program.
Main results: A total of 474 genes were defined in the jujube genome. The amino acid length of the Hsp proteins changes from 75 aa to 2577 aa. The estimated 3-D structure of the ZjuHsp proteins revealed the dominance of the α-helix structure. Phylogenetic tree was constructed to detect evolutionary relationships revealed the eight major groups of the ZjuHsp100 and ZjuHsp60. ZjuHsp proteins could be mainly found in cell parts, membranes, and organelles. It was determined that the ZjuHsp100 genes was targeted by 313 miRNAs.
Highlights: This study helps the researchers who would like to comparative and functional genomic studies.

Keywords

Heat Shock Proteins (Hsp) Ziziphus jujuba Genome Wide Identification Gene Ontology Analysis Phylogenetic Tree

References

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Hünnap Genomunda (Ziziphus jujuba) Isı Şoku Protein Ailelerinin in silico Yöntemler ile Genomik ve Fonksiyonel Karakterizasyonu

Year 2021, Volume: 21 Issue: 3, 277 - 294, 31.12.2021

Yusuf Ceylan , Kevser Betül Ceylan Yasemin Çelik Altunoğlu Mehmet Cengiz Baloğlu

https://doi.org/10.17475/kastorman.1049963
Cited By: 1

Abstract

Çalışmanın amacı : Bu çalıĢmada, genomic yöntemler kullanarak hünnap genomunda yer alan Hsp genlerini tanımlamak ve karakterize etmek amaçlanmıĢtır.
Materyal ve yöntem : NCBI veritabanı kullanılarak Hsp genlerinin protein dizileri elde edilmiĢtir. Genlerin ekzon-intron bölgelerinin tespiti, GSDS program ile yapılmıĢtır. Hsp proteinlerinin korunmuĢ motiflerini ve tahmini üç boyutlu yapılarını tanımlamak için sırasıyla MEME-SUITE ve PHYRE2 programı kullanılmıĢtır. Hsp transkriptlerini hedefleyen miRNA'lar, psRNATarget Server veritabanı kullanılarak tanımlanmıĢtır. Hsp proteinlerinin moleküler fonksiyonu, hücresel bileĢeni ve biyolojik fonksiyonları Blast2GO program ile sunulmuĢtur. Hsp proteinlerinin evrimsel iliĢkilerini belirlemek amacı ile ClustalW yazılımı ile dizi hizalaması yapılmıĢ ve ardından MEGAX program ile filogenetik ağaç çizilmiĢtir.
Temel sonuçlar: Hünnap genomunda toplam 474 gen tanımlanmıĢ ve genler çoğunlukla 1. ve 2. kromozomda dağılım göstermiĢtir. Hsp proteinlerinin amino asit uzunluğu 75 aa (ZjuHsp100-117) ile 2577 aa (ZjuHsp40-104 ve ZjuHsp40-157) arasında değiĢim göstermiĢtir. ZjuHsp proteinlerinin tahmini üç boyutlu yapısında α-sarmal yapısının baskın olduğu görülmüĢtür. Proteinlerin evrimsel iliĢkilerini saptamak için oluĢturulan filogenetik ağaçta, ZjuHsp100 ve ZjuHsp60 grup proteinlerin sekiz ana gruba ayrıldığı gözlenmiĢtir. ZjuHsp proteinlerinin esas olarak hücre kısımlarında, zarlarda, ve organellerde bulunduğu tespit edilmiĢtir. ZjuHsp transkriptlerini hedef alan miRNA'lardan 313'ünün ZjuHsp100 genlerini hedeflediği bulunmuĢtur.
Araştırma vurguları : Bu çalıĢma, karĢılaĢtırmalı ve fonksiyonel genomic çalıĢmalar yapmak isteyen araĢtırmacılara yardımcı olmaktadır.
Anahtar Kelimeler: Isı şoku Proteinleri (Hsp), Ziziphus jujuba, Genom Analizi, Gen Ontoloji Analizi, Filogenetik Ağaç

Keywords

Ziziphus jujuba Genom Analizi Gen Ontoloji Analizi Filogenetik Ağaç Isı şoku Proteinleri (Hsp) Ziziphus jujuba Genom Analizi Gen Ontoloji Analizi Filogenetik Ağaç

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  • Altunoğlu, Y. Ç., Keleş, M., Can, T. H., & Baloğlu, M. C. (2019). Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses. Turkish Journal of Biology, 43(6), 404-419.
  • Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in bipolymers. International Conference on Intelligent Systems for Molecular Biology, 28-36.
  • Baloglu, M. C., Eldem, V., Hajyzadeh, M., & Unver, T. (2014). Genome-wide analysis of the bZIP transcription factors in cucumber. PloS One, 9(4), e96014. doi: 10.1371/journal.pone.0096014.
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  • Çelik Altunoğlu, Y. (2016). Isı Şoku Protein Ailesinden Hsp70 Genlerinin Okaliptüs Genomunda Saptanması ve Karakterizasyonu. Kastamonu Üniversitesi Orman Fakültesi Dergisi, 16(2), 497-509. doi: 10.17475/kastorman.289759.
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  • Chen, J., Gao, T., Wan, S., Zhang, Y., Yang, J., Yu, Y., & Wang, W. (2018). Genome-wide identification, classification and expression analysis of the HSP gene superfamily in tea plant (Camellia sinensis). International Journal of Molecular Sciences, 19(9), 2633. doi: 10.3390/ijms19092633.
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There are 66 citations in total.

Details

Primary Language English
Journal Section Articles
Authors

Yusuf Ceylan

Kevser Betül Ceylan This is me

Yasemin Çelik Altunoğlu This is me

Mehmet Cengiz Baloğlu This is me

Publication Date December 31, 2021
Published in Issue Year 2021 Volume: 21 Issue: 3

Cite

APA Ceylan, Y., Ceylan, K. B., Çelik Altunoğlu, Y., Baloğlu, M. C. (2021). Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty, 21(3), 277-294. https://doi.org/10.17475/kastorman.1049963
AMA Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. December 2021;21(3):277-294. doi:10.17475/kastorman.1049963
Chicago Ceylan, Yusuf, Kevser Betül Ceylan, Yasemin Çelik Altunoğlu, and Mehmet Cengiz Baloğlu. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty 21, no. 3 (December 2021): 277-94. https://doi.org/10.17475/kastorman.1049963.
EndNote Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC (December 1, 2021) Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty 21 3 277–294.
IEEE Y. Ceylan, K. B. Ceylan, Y. Çelik Altunoğlu, and M. C. Baloğlu, “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods”, Kastamonu University Journal of Forestry Faculty, vol. 21, no. 3, pp. 277–294, 2021, doi: 10.17475/kastorman.1049963.
ISNAD Ceylan, Yusuf et al. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty 21/3 (December 2021), 277-294. https://doi.org/10.17475/kastorman.1049963.
JAMA Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. 2021;21:277–294.
MLA Ceylan, Yusuf et al. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty, vol. 21, no. 3, 2021, pp. 277-94, doi:10.17475/kastorman.1049963.
Vancouver Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. 2021;21(3):277-94.

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