Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana

Abstract

Advances in next-generation sequencing technologies facilitate the study of plant molecular functions in detail and with precision. Plant genome and proteome databases are continually being updated with large transcriptomic or genomic datasets. With the ever-increasing amount of sequencing data, several thousands of genes or proteins in public databases remain uncharacterized, and their domain functions are largely unknown. Such proteins contain domains of unknown function (DUF). In the present study, we identified 231 upregulated and 206 downregulated DUF genes from the available RNA-Seq-based transcriptome profiling datasets of Arabidopsis leaves exposed to a nitric oxide donor, S -nitroso-L-cysteine (CysNO). In addition, we performed extensive in silico and biological experiments to determine the potential functions of AtDUF569 and to elucidate its role in plant growth, development, and defense. We validated the expression pattern of the most upregulated and the most downregulated DUF genes from the transcriptomic data. In addition, a loss-of AtDUF569 function mutant was evaluated for growth, development, and defense against biotic and abiotic stresses. According to the results of the study, AtDUF569 negatively regulates biotic stress responses and differentially regulates plant growth under nitro-oxidative stress conditions.

The Transcriptomic and Bioinformatic Characterizations of Iron Acquisition and Heme Utilization in Avibacterium paragallinarum in Response to Iron-Starvation

“…Even when sequencing data is being increased, there are also a lot of genes or proteins that are uncharacterized and their domain functions are unknown ( Nabi et al, 2020 ). These proteins are regarded as proteins having DUFs ( Finn et al, 2016 ; El-Gebali et al, 2019 ).…”

A Novel DUF569 Gene Is a Positive Regulator of the Drought Stress Response in Arabidopsis

“…All plants were grown at 22 ± 2 °C under long day photoperiod (with a 16:8 h light: dark). Plants were genotyped using T-DNA left border primers and gene-specific primers to identify homozygous mutant plants as described previously [ 39 ]. Arabidopsis seeds were germinated and grown on a peat moss substrate mixture with perlite and vermiculite (in a 1:1 ratio).…”

“…Leaf tissue samples from the drought and control conditions were collected at two time points (3 and 7 days). Total RNA was extracted using the method described [ 39 ]. In brief, total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA, USA), and the extracted RNA was used with reverse transcriptase kits (BIOFACT, Daejeon, Korea) to synthesize first-strand complementary DNA (cDNA) according to the kit manufacturer’s instructions.…”

“…Previously, we identified a connection between DUF genes and NO following transcriptomic analysis of Arabidopsis leaves in response to NO accumulation [ 38 , 39 ]. Based on the highest fold change (57.29) we selected novel DUF569 (AT1G69890) as a protein-coding gene for further characterization.…”

Genetic Diversity Analysis of Korean Peanut Germplasm Using 48 K SNPs ‘Axiom_Arachis’ Array and Its Application for Cultivar Differentiation

“…High-quality genomic DNA extraction was performed using a Quigene DNA kit (Nucleospain, Plant 11-Ref; 740770.250; Lot No: 1909/001) with minor modi cations. DNA quality and quantity were assessed as reported previously [39].…”