拟南芥一氧化氮诱导的 NBS-LRR 基因的全基因组特征及其在单子叶植物和双子叶植物中的关联。

Genome-wide characterization of nitric oxide-induced NBS-LRR genes from Arabidopsis thaliana and their association in monocots and dicots.

机构信息

Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, South Korea.

Department of Agriculture, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan.

出版信息

BMC Plant Biol. 2024 Oct 9;24(1):934. doi: 10.1186/s12870-024-05587-3.

DOI:10.1186/s12870-024-05587-3

PMID:39379841

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11462825/

Abstract

BACKGROUND

Nitric oxide (NO) is pivotal in regulating the activity of NBS-LRR specific R genes, crucial components of the plant's immune system. It is noteworthy that previous research has not included a genome-wide analysis of NO-responsive NBS-LRR genes in plants.

RESULTS

The current study examined 29 NO-induced NBS-LRR genes from Arabidopsis thaliana, along with two monocots (rice and maize) and two dicots (soybean and tomato) using genome-wide analysis tools. These NBS-LRR genes were subjected to comprehensive characterization, including analysis of their physio-chemical properties, phylogenetic relationships, domain and motif identification, exon/intron structures, cis-elements, protein-protein interactions, prediction of S-Nitrosylation sites, and comparison of transcriptomic and qRT-PCR data. Results showed the diverse distribution of NBS-LRR genes across chromosomes, and variations in amino acid number, exons/introns, molecular weight, and theoretical isoelectric point, and they were found in various cellular locations like the plasma membrane, cytoplasm, and nucleus. These genes predominantly harbor the NB-ARC superfamily, LRR, LRR_8, and TIR domains, as also confirmed by motif analysis. Additionally, they feature species-specific PLN00113 superfamily and RX-CC_like domain in dicots and monocots, respectively, both responsive to defense against pathogen attacks. The NO-induced NBS-LRR genes of Arabidopsis reveal the presence of cis-elements responsive to phytohormones, light, stress, and growth, suggesting a wide range of responses mediated by NO. Protein-protein interactions, coupled with the prediction of S-Nitrosylation sites, offer valuable insights into the regulatory role of NO at the protein level within each respective species.

CONCLUSION

These above findings aimed to provide a thorough understanding of the impact of NO on NBS-LRR genes and their relationships with key plant species.

摘要

背景

一氧化氮（NO）在调节植物免疫系统中 NBS-LRR 特异性 R 基因的活性方面起着关键作用。值得注意的是，之前的研究并未包括对植物中 NO 响应的 NBS-LRR 基因进行全基因组分析。

结果

本研究使用全基因组分析工具，从拟南芥中检查了 29 个 NO 诱导的 NBS-LRR 基因，以及两种单子叶植物（水稻和玉米）和两种双子叶植物（大豆和番茄）。这些 NBS-LRR 基因进行了全面表征，包括它们的理化性质、系统发育关系、结构域和基序鉴定、外显子/内含子结构、顺式元件、蛋白质-蛋白质相互作用、S-亚硝酰化位点预测以及转录组和 qRT-PCR 数据的比较。结果表明，NBS-LRR 基因在染色体上的分布多样化，并且在氨基酸数量、外显子/内含子、分子量和理论等电点上存在差异，它们存在于各种细胞位置，如质膜、细胞质和细胞核。这些基因主要包含 NB-ARC 超家族、LRR、LRR_8 和 TIR 结构域，这也通过基序分析得到了证实。此外，它们在双子叶植物和单子叶植物中分别具有特定于物种的 PLN00113 超家族和 RX-CC_like 结构域，均对防御病原体攻击具有反应性。拟南芥中 NO 诱导的 NBS-LRR 基因揭示了对植物激素、光照、胁迫和生长响应的顺式元件的存在，表明 NO 介导了广泛的反应。蛋白质-蛋白质相互作用，加上 S-亚硝酰化位点的预测，为 NO 在每个物种的蛋白质水平上的调节作用提供了有价值的见解。