Transcriptome wide identification and characterization of NO-responsive WRKY transcription factors in <i>Arabidopsis thaliana</i> L.

Imran, Qari Muhammad,Hussain, Adil,Mun, Bong-Gyu,Lee, Sang Uk,Asaf, Sajjad,Ali, Muhammad Amjad,Lee, In-Jung,Yun, Byung-Wook Elsevier 2018 Environmental and experimental botany Vol.148 No.-

<P><B>Abstract</B></P> <P>WRKY transcription factors are important plant-specific regulatory genes characterized by one or two conserved WRKY domain(s) usually followed by a zinc-finger motif. In this study using <I>Arabidopsis thaliana</I>, the RNA-Seq based transcriptomic analysis showed differential expression of 33 genes encoding WRKY TFs in response to the nitric oxide (NO) donor S-Nitrosocysteine (CySNO). Interestingly, 93.9% of these TFs were up-regulated with at least 2-fold change, suggesting their putative involvement in NO mediated gene regulation. GO- analysis of all the 33 transcriptomic elements showed their putative involvement in biological processes such as abiotic stress tolerance and defense against fungal pathogens (89.39 fold enrichment). Analysis of the NO-responsive AtWRKY TFs promoter region revealed the presence of the <I>cis</I>-acting elements such as ABRE, EIRE, ERE, and MBS involved in osmotic stress response, maximal elicitor-mediated activation, and drought-stress regulation. The analysis of NO-responsive AtWRKY TF motifs and their comparison with rice, soybean, and tomato orthologs suggested that members of the WRKY family belonging to the same group shared similar motifs and phylogenetic tree suggested that these TFs were highly conserved. Validation of transcriptomic data through quantitative real time-PCR showed a high correlation coefficient (0.85) indicating the high reliability and similarity of both types of analysis. Comparison of the NO-responsive and non-responsive WRKYs showed the presence of tyrosine (T) and cysteine (C) residues at a distance of 7 residues from the WRKYGQK motif which may serve as potential targets for modification by NO via tyrosine nitration and S-nitrosylation. We also validated the response of WRKYs through <I>in vivo</I> analysis using <I>atwrky62</I> loss of function mutant and the results indicated a negative role of <I>AtWRKY62</I> in plant growth. Furthermore, <I>atwrky62</I> showed significantly less SNO contents compared to wild type plants indicating putative role of <I>AtWRKY</I>62 in NO metabolism.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The expression of more than 90% of the NO-responsive WRKY TFs was up-regulated within 6 h of CySNO infiltration. </LI> <LI> NO-responsive AtWRKY TFs share a high sequence homology with those of rice, tomato and soybean suggesting a similar conserved function for these WRKYs among the species. </LI> <LI> GO terms for biological processes associated majority of NO-responsive WRKYs to GO term for response to fungal stimuli. </LI> <LI> Most of the NO-responsive WRKY TFs have either Cysteine or Tyrosine residues (potential targets for protein <I>S</I>-nitrosylation) at 7<SUP>th</SUP> position from WRKY motif while NO-non-responsive don’t have these residues. </LI> <LI> <I>atwrky62</I> loss-of-function mutants negatively regulates shoot and root length under control and CySNO induced nitrosative stress. </LI> </UL> </P>

Pathogen-induced Defense Strategies in Plants

Qari Muhammad Imran,윤병욱 한국작물학회 2020 Journal of crop science and biotechnology Vol.23 No.2

Plants are the ultimate producers of this ecosystem and effect human life directly and/or indirectly. However, being sessile organisms, plants are susceptible to several adverse environmental conditions and pathogen ingress resulting in huge losses to yield and productivity. Therefore, plans are continuously evolving complex regulatory networks to respond to these environmental changes. Due to its impact on pre- and post-harvest losses, biotic stress is of great concern to plant scientists. Interpreting the underlying mechanism of plant response to biotic stresses is therefore of great importance. A brief account about these hostile conditions and plants responses towards them is described in this review.

Effects of plant-derived smoke on the growth dynamics of Barnyard Grass (Echinochloa crus-galli)

Kamran, Muhammad,Khan, Abdul Latif,Waqas, Muhammad,Imran, Qari Muhammad,Hamayun, Muhammad,Kang, Sang-Mo,Kim, Yoon-Ha,Kim, Min-Ji,Lee, In-Jung Taylor Francis 2014 Acta agriculturæ Scandinavica. Section B, So Vol.64 No.2

Nitric oxide-induced AtAO3 differentially regulates plant defense against Pseudomonas syringae pv. tomato in Arabidopsis thaliana

Murtaza Khan,Qari Muhammad Imran,Muhammad Shahid,Bong-Gyu Mun,Byung-Wook Yun 한국농약과학회 2018 한국농약과학회 학술발표대회 논문집 Vol.2018 No.10

Regulation of endogenous phytohormones and essential metabolites in frankincense-producing Boswellia sacra under wounding stress

Khan, Abdul Latif,Al-Harrasi, Ahmed,Shahzad, Raheem,Imran, Qari Muhammad,Yun, Byung-Wook,Kim, Yoon-Ha,Kang, Sang-Mo,Al-Rawahi, Ahmed,Lee, In-Jung Springer-Verlag 2018 ACTA PHYSIOLOGIAE PLANTARUM Vol.40 No.6

Profile and Time-Scale Dynamics of Differentially Expressed Genes in Transcriptome of Populus davidiana Under Drought Stress

Mun, Bong-Gyu,Hussain, Adil,Park, Eung-Jun,Lee, Sang-Uk,Sharma, Arti,Imran, Qari Muhammad,Jung, Ki-Hong,Yun, Byung-Wook Springer-Verlag 2017 Plant molecular biology reporter Vol.35 No.6

<P>The genus Populus contains 25-35 species of deciduous flowering plants in the family Salicaceae. It has evolved to overcome various environmental stresses including drought stress through changes in physiological processes such a stomatal movement, photosynthesis, stress signaling, defense responses, and overall growth rate. In this study, we performed RNA-seq-based transcriptome profiling of Populus davidiana in response to drought stress induced by 10% PEG at two time points (6 and 12 h). We generated over 527 million reads by applying Populus trichocarpa as reference genome. Assembly of the reads yielded 32,650 genes and 75,820 transcripts; of these, after quantile normalization, a total of 997 genes were identified with dynamic expression over time, classifying them into nine different clusters. Among them, 550 genes responded significantly to drought stress treatment after 6 h (108 genes up-regulated and 201 genes down-regulated) and 12 h (161 up-regulated and 80 down-regulated) respectively, with at least twofold change in their expression. Based on analysis of these genes, we found several differentially expressed genes (DEGs) involved in cellular transport, transcriptional regulation, protein modification, regulation of cellular redox state, and those involved in response to other stresses. We also validated RNA-seq-mediated transcriptome data by RT-qPCR analysis of eight randomly selected DEGs. It showed significantly high correlation coefficient (0.95) suggesting high reliability of RNA-seq analysis. This study presents the first RNA-seq mediated transcriptome profile of P. davidiana in response to drought stress, providing critical information necessary for understanding the mechanisms underpinning drought stress tolerance in forest trees and other plant species.</P>

Analysis of transcription factors among differentially expressed genes induced by drought stress in <i>Populus davidiana</i>

Mun, Bong-Gyu,Lee, Sang-Uk,Park, Eung-Jun,Kim, Hyun-Ho,Hussain, Adil,Imran, Qari Muhammad,Lee, In-Jung,Yun, Byung-Wook Springer Berlin Heidelberg 2017 3 Biotech Vol.7 No.3

<P><I>Populus davidiana</I> is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other <I>Populus</I> species such as <I>P. trichocarpa, P. euphratica,</I> and <I>P. tremula</I>, relatively little is known about <I>P. davidiana.</I> Here, we performed transcriptomic analysis of <I>P. davidiana</I> under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the <I>P. trichocarpa</I> reference genome after 6 and 12 h of treatment, respectively. Of these, a total of 404 genes (238 up-regulated and 166 down-regulated) after 6 h and 359 genes (187 up-regulated and 172 down-regulated) after 12 h of treatment were identified as transcription factors. Transcription factors known to be key genes for drought stress response, such as AP2-EREB, WRKY, C2H2, and NAC, were identified. This results suggesting that early induction of these genes affected initiation of transcriptional regulation in response to drought stress. Quantitative real-time PCR results of selected genes showed highly significant (<I>R</I> = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was <I>P. davidiana</I> specific. The sequence of <I>P. davidiana</I> ortholog of <I>P. trichocarpa</I> gene POPTR_0018s10230, which plays an important role in plant response to drought, was further analyzed as our RNA-Seq results showed highly significant changes in the expression of this gene following the stress treatment. Sequence of the gene was compared to <I>P. trichocarpa</I> gene sequence using cloning-based sequencing. Additionally, we generated a predicted 3D protein structure for the gene product. Results indicated that the amino acid sequence of <I>P. davidiana</I>-specific POPTR_0018s10230 is different at six different positions compared to <I>P. trichocarpa</I>, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in <I>P. davidiana</I> under drought stress will not only offer clues for understanding the underlying mechanisms involved in drought stress physiology but also serve as a basis for future molecular studies on this species.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s13205-017-0858-7) contains supplementary material, which is available to authorized users.</P>