Sains Malaysiana 50(9)(2021): 2591-2602

http://doi.org/10.17576/jsm-2021-5009-08

In-silico Characterization and Expression Analysis of NB-ARC Genes in Response to Erwinia mallotivora in Carica papaya

(Pencirian In-silico dan Analisis Pengekspresan Gen NB-ARC sebagai Gerak Balas kepada Erwinia mallotivora pada Carica papaya)

NUR SYAZANA ABU BAKAR¹, NOOR BAITY SAIDI^1,3, LINA ROZANO², MOHD PUAD ABDULLAH¹ & SUHAINA SUPIAN^2*

¹Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia

²Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400 Serdang, Selangor Darul Ehsan, Malaysia

³Biodiversity Unit, Institute of Biosciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia

Received: 20 October 2020/Accepted: 21 January 2021

ABSTRACT

Disease resistance in plants is commonly associated with resistance (R) genes that encode nucleotide binding site-leucine rich repeat (NBS-LRR) domains that are essential for pathogen recognition and defence signalling. In this study, we identified and analyzed the sequence of putative pathogen-responsive NB-ARC transcripts from Carica papaya transcriptome database, carried out the structural and phylogenetic analysis, and determined the expression profile of the transcripts in C. papaya challenged with Erwinia mallotivora. The findings indicate CpNBS1, the only pathogen-responsive NB-ARC protein identified in this study belongs to the CC-NBS-LRR group. Semi-quantitative PCR showed CpNBS1 was differentially expressed in response to E. mallotivora. Structural analysis of the 4993-Eksotika and 4993-Viorica translated proteins showed striking differences in terms of the number of β-sheets and α-helixes as well their ligand-binding surface, suggesting the role of the LRR domain in determining the specificity of recognition of E. mallotivora effector. Collectively, this study provides new insights into the role of NBS-LRR genes in C. papaya and its implications for enhancing of plant disease resistance through genetic engineering.

Keywords: E. mallotivora; nucleotide binding site-leucine rich repeat; resistance gene

ABSTRAK

Kerintangan penyakit pada tumbuhan sering dikaitkan dengan gen kerintangan (R) yang mempunyai domain tapak pengikat nukleotida-ulangan kaya leusina(NBS-LRR) yang berperanan untuk mengenal pasti patogen dan isyarat pertahanan. Dalam kajian ini, kami mengenal pasti dan menganalisis jujukan daripada pangkalan data transkriptomCarica papaya, menjalankan analisis struktur dan filogenetik serta memprofil pengekspresan transkripC. papaya yang telah dicabar denganErwinia mallotivora. Keputusan kajian ini menunjukkan bahawa CpNBS1 adalah satu-satunya protein yang bergerak balas terhadap patogen dan berada dalam kumpulan CC-NBS-LRR. Analisis separa-kuantitatif PCR menunjukkan bahawa CpNBS1 telah diungkapkan secara berbeza sebagai gerak balas kepadaE. mallotivora. Analisis struktur pula menunjukkan perbezaan yang nyata daripada segi bilangan kepingan beta dan heliks alfa serta permukaan ikatan ligan, yang mencadangkan peranan domain LRR dalam menentukan ketepatan pengecaman efektor E. mallotivora. Secara keseluruhannya, kajian ini mendedahkan pandangan baharu fungsi gen NBS-LRR dalamC. papaya dan kesannya kepada penambahbaikan kerintangan penyakit dalam tumbuhan melalui kejuruteraan genetik.

Kata kunci: E. mallotivora; gen kerintangan; tapak pengikat nukleotida-ulangan kaya leusina

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*Corresponding author; email: suhaina@mardi.gov.my