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  • 1. Al Azzawi, Tiba Nazar Ibrahim
    et al.
    Khan, Murtaza
    Hussain, Adil
    Shahid, Muhammad
    Imran, Qari Muhammad
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik. School of Applied Biosciences, Kyungpook National University, Korea.
    Mun, Bong-Gyu
    Lee, Sang-Uk
    Yun, Byung-Wook
    Evaluation of Iraqi Rice Cultivars for Their Tolerance to Drought Stress2020Inngår i: Agronomy, E-ISSN 2073-4395, Vol. 10, nr 11, artikkel-id 1782Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Drought stress is a serious problem around the globe and particularly in the Republic of Iraq. Rice is the third most consumed crop for the Iraqi people; however, its cultivation and production is very low due to several challenges including drought. The current study was performed to evaluate five Iraqi rice cultivars along with relevant (drought-tolerant and drought-susceptible) controls under drought stress, either by treatment with 10% PEG (polyethylene glycol) or through water withholding to induce natural drought stress. The phenotypes of all the cultivars were evaluated and the transcriptional responses of key drought-responsive candidate genes, identified through the EST-SSR marker-based approach, were studied. We also studied transcript accumulation of drought-related transcriptional factors, such as OsGRASS23, OsbZIP12, and OsDREB2A. Moreover, the reference cultivars also included a drought-tolerant inter-specific cultivar Nerica 7 (a cross between Oryza sativa ssp. indica X O. glaberrima). Among the cultivars, the more drought-tolerant phenotypic characteristics and higher transcript accumulation of drought-related marker genes OsE647 and OsE1899 and transcriptional factors OsGRASS23, OsbZIP12, and OsDREB2A were observed in four (out of five) significantly drought-tolerant Iraqi cultivars; Mashkab, followed by Furat, Yasmen, and Amber 33. On another note, Amber Barka was found to be significantly drought susceptible. Mashkab and Amber Barka were found to be the most drought-tolerant and-susceptible cultivars, respectively. The identified tolerant cultivars may potentially serve as a genetic source for the incorporation of drought-tolerant phenotypes in rice.

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  • 2. Ali, Muhammad Amjad
    et al.
    Azeem, Farrukh
    Nawaz, Muhammad Amjad
    Acet, Tuba
    Abbas, Amjad
    Imran, Qari Muhammad
    Laboratory of Plant Functional Genomics, College of Agriculture & Life Sciences, Kyngpook National University, Buk-gu Daegu, South Korea.
    Shah, Kausar Hussain
    Rehman, Hafiz Mamoon
    Chung, Gyuhwa
    Yang, Seung Hwan
    Transcription factors WRKY11 and WRKY17 are involved in abiotic stress responses in Arabidopsis2018Inngår i: Journal of plant physiology (Print), ISSN 0176-1617, E-ISSN 1618-1328, Vol. 226, s. 12-21Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plant WRKY transcription factors play a vital role in abiotic stress tolerance and regulation of plant defense responses. This study examined AtWRKY11 and AtWRKY17 expression under ABA, salt, and osmotic stress at different developmental stages in Arabidopsis. We used reverse transcriptase PCR, quantitative real-time PCR, and promoter:GUS lines to analyze expression. Both genes were upregulated in response to abiotic stress. Next, we applied the same stressors to seedlings of T-DNA insertion wrky11 and 17 knock-out mutants (single and double). Under stress, the mutants exhibited slower germination and compromised root growth compared with the wild type. In most cases, double-mutant seedlings were more affected than single mutants. These results suggest that wrky11 and wrky17 are not strictly limited to plant defense responses but are also involved in conferring stress tolerance.

  • 3. Asaf, Sajjad
    et al.
    Khan, Abdul Latif
    Aaqil Khan, Muhammad
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
    Kang, Sang-Mo
    Al-Hosni, Khdija
    Jeong, Eun Ju
    Lee, Ko Eun
    Lee, In-Jung
    Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species2017Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 12, nr 8Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of Gsoja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The Gsoja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between Gmax and Ggracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with Gcyrtoloba. The sequence of the accD gene from Gsoja was highly divergent from those of the other species except for Gmax and Ggracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that Gsoja is closely related to Gmax and Ggracilis. The complete Gsoja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.

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  • 4. Asaf, Sajjad
    et al.
    Khan, Abdul Latif
    Khan, Muhammad Aaqil
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.
    Yun, Byung-Wook
    Lee, In-Jung
    Osmoprotective functions conferred to soybean plants via inoculation with Sphingomonas sp. LK11 and exogenous trehalose2017Inngår i: Microbiology Research, ISSN 0944-5013, E-ISSN 1618-0623, Vol. 205, s. 135-145Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Osmotic stress induced by drought can hinder the growth and yield of crop plants. To understand the eco-physiological role of osmoprotectants, the combined utilization of endophytes and osmolytes (trehalose) can be an ideal strategy used to overcome the adverse effects of drought. Hence, in the present study, we aimed to investigate the role of Sphingomonas sp. LK11, which produces phytohormones and synthesizes trehalose, in improving soybean plant growth under drought-induced osmotic stress (−0.4, −0.9, and −1.2 MPa). The results showed that the inoculation of soybean plants with Sphingomonas sp. LK11 significantly increased plant length, dry biomass, photosynthetic pigments, glutathione, amino acids (proline, glycine, and glutamate), and primary sugars as compared to control plants under varying drought stresses. Trehalose applied to the plant with or without endophyte-inoculation also showed similar plant growth-promoting attributes under stress. Stress exposure significantly enhanced endogenous jasmonic (JA) and abscisic (ABA) acid contents in control plants. In contrast, Sphingomonas sp. LK11-inoculation significantly lowered ABA and JA levels in soybean plants, but these phytohormones increased in response to combined treatments during stress. The drought-induced osmotic stress resistance associated with Sphingomonas sp. LK11 and trehalose was also evidenced by increased mRNA gene expression of soybean dehydration responsive element binding protein (DREB)-type transcription factors (GmDREBa and GmDREB2) and the MYB (myeloblastosis) transcription factor (GmMYBJ1) as compared to the control. In conclusion, our findings demonstrated that inoculation with this endophyte and trehalose improved the negative effects of drought-induced osmotic stress, and it enhanced soybean plant growth and tolerance.

  • 5. Asaf, Sajjad
    et al.
    Waqas, Muhammad
    Khan, Abdul L.
    Khan, Muhammad A.
    Kang, Sang-Mo
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Shahzad, Raheem
    Bilal, Saqib
    Yun, Byung-Wook
    Lee, In-Jung
    The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species2017Inngår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, artikkel-id 304Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the Ominuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete Ominuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

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  • 6. Bilal, Saqib
    et al.
    Shahzad, Raheem
    Khan, Abdul L
    Kang, Sang-Mo
    Imran, Qari Muhammad
    Al-Harrasi, Ahmed
    Yun, Byung-Wook
    Lee, In-Jung
    Endophytic microbial consortia of phytohormones-producing fungus Paecilomyces formosus LHL10 and bacteria Sphingomonas sp. LK11 to Glycine max L. regulates physio-hormonal changes to attenuate aluminum and zinc stresses2018Inngår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 9, artikkel-id 1273Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The compatible microbial consortia containing fungal and bacterial symbionts acting synergistically are applied to improve plant growth and eco-physiological responses in extreme crop growth conditions. However, the interactive effects of phytohormones-producing endophytic fungal and bacterial symbionts plant growth and stress tolerance under heavy metal stress have been least known. In the current study, the phytohormones-producing endophytic Paecilomyces formosus LHL10 and Sphingomonas sp. LK11 revealed potent growth and tolerance during their initial screening against combined Al and Zn (2.5 mM each) stress. This was followed with their co-inoculation in the Al- and Zn-stressed Glycine max L. plants, showing significantly higher plant growth attributes (shoot/root length, fresh/dry weight, and chlorophyll content) than the plants solely inoculated with LHL10 or LK11 and the non-inoculated (control) plants under metal stresses. Interestingly, under metal stress, the consortia exhibited lower metal uptake and inhibited metal transport in roots. Metal-induced oxidative stresses were modulated in co-inoculated plants through reduced hydrogen peroxide, lipid peroxidation, and antioxidant enzymes (catalase and superoxide dismutase) in comparison to the non-inoculated plants. In addition, endophytic co-inoculation enhanced plant macronutrient uptake (P, K, S, and N) and modulated soil enzymatic activities under stress conditions. It significantly downregulated the expression of heavy metal ATPase genes GmHMA13, GmHMA18, GmHMA19, and GmPHA1 and upregulated the expression of an ariadne-like ubiquitin ligase gene GmARI1 under heavy metals stress. Furthermore, the endogenous phytohormonal contents of co-inoculated plants revealed significantly enhanced gibberellins and reduced abscisic acid and jasmonic acid contents, suggesting that this endophytic interaction mitigated the adverse effect of metal stresses in host plants. In conclusion, the co-inoculation of the endophytic fungus LHL10 and bacteria LK11 actively contributed to the tripartite mutualistic symbiosis in G. max under heavy metal stresses; this could be used an excellent strategy for sustainable agriculture in the heavy metal-contaminated fields.

  • 7.
    Blomberg, Jeanette
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Tasselius, Viktor
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik. Biostatistics, School of Public Health and Community Medicine, Gothenburg University, Gothenburg, Sweden.
    Vergara, Alexander
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Karamat, Fazeelat
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Imran, Qari Muhammad
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Rosvall, Martin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Björklund, Stefan
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Pseudomonas syringae infectivity correlates to altered transcript and metabolite levels of Arabidopsis mediator mutants2024Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 14, nr 1, artikkel-id 6771Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16, med18, med25 and cdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in med16 and cdk8, but increased in med25, which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that MED16, MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infections.

    Fulltekst (pdf)
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  • 8. Bot, Phearom
    et al.
    Mun, Bong-Gyu
    Imran, Qari Muhammad
    Hussain, Adil
    Lee, Sang-Uk
    Loake, Gary
    Yun, Byung-Wook
    Differential expression of AtWAKL10 in response to nitric oxide suggests a putative role in biotic and abiotic stress responses2019Inngår i: PeerJ, Vol. 7Artikkel i tidsskrift (Fagfellevurdert)
  • 9. Falak, Noreen
    et al.
    Imran, Qari Muhammad
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik. Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, Korea.
    Hussain, Adil
    Yun, Byung-Wook
    Transcription Factors as the "Blitzkrieg" of Plant Defense: A Pragmatic View of Nitric Oxide's Role in Gene Regulation2021Inngår i: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 22, nr 2, artikkel-id 522Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Plants are in continuous conflict with the environmental constraints and their sessile nature demands a fine-tuned, well-designed defense mechanism that can cope with a multitude of biotic and abiotic assaults. Therefore, plants have developed innate immunity, R-gene-mediated resistance, and systemic acquired resistance to ensure their survival. Transcription factors (TFs) are among the most important genetic components for the regulation of gene expression and several other biological processes. They bind to specific sequences in the DNA called transcription factor binding sites (TFBSs) that are present in the regulatory regions of genes. Depending on the environmental conditions, TFs can either enhance or suppress transcriptional processes. In the last couple of decades, nitric oxide (NO) emerged as a crucial molecule for signaling and regulating biological processes. Here, we have overviewed the plant defense system, the role of TFs in mediating the defense response, and that how NO can manipulate transcriptional changes including direct post-translational modifications of TFs. We also propose that NO might regulate gene expression by regulating the recruitment of RNA polymerase during transcription.

    Fulltekst (pdf)
    fulltext
  • 10.
    Hussain, Adil
    et al.
    Department of Agriculture, Abdul Wali Khan University, Khyber Pakhtunkhwa, Mardan, Pakistan.
    Imran, Qari Muhammad
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik. School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Shahid, Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea; Agriculture Research Institute, Khyber Pakhtunkhwa, Mingora, Pakistan.
    Yun, Byung-Wook
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Nitric oxide synthase in the plant kingdom2021Inngår i: Nitric oxide in plant biology: an ancient molecule with emerging roles / [ed] Vijay Pratap Singh; Samiksha Singh; Durgesh Kumar Tripathi; Maria C. Romero-Puertas; Luisa Sandalio, Elsevier, 2021, s. 43-52Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    After the discovery of nitric oxide (NO) as an important signaling molecule in plants, its involvement has been reported in several key physiological processes. At the cellular level, slight alterations in the quantity of NO or its various adducts, also known as reactive nitrogen intermediates (RNIs), have phenomenal implications. In plants this highly reactive, diatomic gaseous molecule regulates a plethora of physiological processes ranging from development, to reproduction, and defense against biotic and abiotic stresses. In animals, NO is produced enzymatically via the nitric oxide synthase (NOS) enzyme. However, after decades of research, it is now clear that in plants there is not one but several routes for NO production. Interestingly the discovery of a NOS enzyme in plants has remained an attractive topic of research for plant scientists over the years; the enzyme still remains elusive. In this chapter we briefly discuss the different pathways responsible for NO production in plants with special emphasis on the enzymatic production. We also discuss the NOS enzyme and its presence in lower and higher plants.

  • 11. Hussain, Adil
    et al.
    Imran, Qari Muhammad
    School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Republic of Korea.
    Yun, Byung-Wook
    CRISPR/Cas9-mediated gene editing in grain crops2020Inngår i: Recent Advances in Grain Crops Research, IntechOpen , 2020, s. 1-12Kapittel i bok, del av antologi (Annet vitenskapelig)
    Abstract [en]

    The development of reliable and efficient techniques for making precise targeted changes in the genome of living organisms has been a long-standing objective of researchers throughout the world. In plants, different methods, each with several different variations, have been developed for this purpose, though many of them are hampered either by providing only temporary modification of gene function or unpredictable off-target results. The recent discovery of clustered regularly interspaced short palindromic repeats (CRISPRs) and the CRISPR-associated 9 (Cas9) nucleases started a new era in genome editing. Basically, the CRISPR/Cas system is a natural immune response of prokaryotes to resist foreign genetic elements entering via plasmids and phages. Through this naturally occurring gene editing system, bacteria create DNA segments known as CRISPR arrays that allow them to "remember" foreign genetic material for protection against it and other similar sequences in the future. This system has now been adopted by researchers in laboratory to create a short guide RNA that binds to specific target sequences of DNA in eukaryotic genome, and the Cas9 enzyme cuts the DNA at the targeted location. Once cut, the cell's endogenous DNA repair machinery is used to add, delete, or replace pieces of genetic material. Though CRISPR/Cas9 technology has been recently developed, it has started to be regularly used for gene editing in plants as well as animals to good success. It has been proved as an efficient transgene-free technique. A simple search on PubMed (NCBI) shows that among all plants, 80 different studies published since 2013 involved CRISPR/Cas9-mediated genome editing in rice. Of these, 20, 13, and 24 papers have been published in 2019, 2018, and 2017, respectively. Furthermore, 20 different studies published since 2014 utilized CRISPR/Cas9 system for gene editing in wheat, where five of these studies were published in 2019 and seven were published in 2018. Genomes of other grain crops edited through this technique include maize, sorghum, barley, etc. This indicates the high utility of this technique for gene editing in grain crops. Here we emphasize on CRISPR/Cas9-mediated gene editing in rice, wheat, and maize.

  • 12. Hussain, Adil
    et al.
    Mun, Bong-Gyu
    Imran, Qari Muhammad
    Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, South Kore.
    Lee, Sang-Uk
    Adamu, Teferi A.
    Shahid, Muhammad
    Kim, Kyung-Min
    Yun, Byung-Wook
    Nitric oxide mediated transcriptome profiling reveals activation of multiple regulatory pathways in Arabidopsis thaliana2016Inngår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Imbalance between the accumulation and removal of nitric oxide and its derivatives is a challenge faced by all plants at the cellular level, and is especially important under stress conditions. Exposure of plants to various biotic and abiotic stresses causes rapid changes in cellular redox tone potentiated by the rise in reactive nitrogen species that serve as signaling molecules in mediating defensive responses. To understand mechanisms mediated by these signaling molecules, we performed a large-scale analysis of the Arabidopsis transcriptome induced by nitrosative stress. We generated an average of 84 and 91 million reads from three replicates each of control and 1 mM S-nitrosocysteine (CysNO)-infiltrated Arabidopsis leaf samples, respectively. After alignment, more than 95% of all reads successfully mapped to the reference and 32,535 genes and 55,682 transcripts were obtained. CysNO infiltration caused differential expression of 6436 genes (3448 up-regulated and 2988 down-regulated) and 6214 transcripts (3335 up-regulated and 2879 down-regulated) 6 h post-infiltration. These differentially expressed genes were found to be involved in key physiological processes, including plant defense against various biotic and abiotic stresses, hormone signaling, and other developmental processes. After quantile normalization of the FPKM values followed by student's T-test (P < 0.05) we identified 1165 DEGs (463 up-regulated and 702 down-regulated) with at least 2-folds change in expression after CysNO treatment. Expression patterns of selected genes involved in various biological pathways were verified using quantitative real-time PCR. This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants.

    Fulltekst (pdf)
    fulltext
  • 13.
    Imran, Muhammad
    et al.
    School of Applied Biosciences, Kyungpook National University, South Korea.
    Shazad, Raheem
    Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.
    Bilal, Saqib
    Department of Horticulture, University of Haripur, Haripur, Pakistan.
    Imran, Qari Muhammad
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Khan, Murtaza
    School of Applied Biosciences, Kyungpook National University, South Korea.
    Kang, Sang-Mo
    School of Applied Biosciences, Kyungpook National University, South Korea.
    Khan, Abdul Latif
    Department of Horticulture, University of Haripur, Haripur, Pakistan.
    Yun, Byung-Wook
    School of Applied Biosciences, Kyungpook National University, South Korea.
    Lee, In-Jung
    School of Applied Biosciences, Kyungpook National University, South Korea.
    Exogenous Melatonin mediates the regulation of endogenous nitric oxide in Glycine max L. to reduce effects of drought stress2021Inngår i: Environmental and Experimental Botany, ISSN 0098-8472, E-ISSN 1873-7307, Vol. 188, artikkel-id 104511Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Drought stress retards plant growth and yield. Melatonin and nitric oxide (NO) have demonstrated their potential role against abiotic stresses; however, the underlying molecular mechanism by which they interact and extend drought stress tolerance has not been fully elucidated. Herein, the current study was performed to establish the optimum beneficial concentration of MT and NO in combating drought stress and later understand its responses at biochemical, and molecular levels. Results showed exogenous MT, and sodium nitroprusside (SNP as NO donor) have counteracted drought-induced growth inhibition of soybean (Glycine max L.) by increasing plant biomass, photosynthesis efficiency and water content and reducing reactive oxygen species accumulation. MT and NO treatments showed reduced lipid peroxidation and improved defense responses via significantly higher antioxidant enzyme activities than control during drought. Surprisingly, endogenous abscisic acid (ABA) contents and gene expression of its synthesis and ABA-responsive proteins and their promoters were significantly decreased in drought by MT + NO. This was coupled with an increase in endogenous MT levels. In endo-NO regulations, S-nitrosoglutathione was increased, but L-NAME (NO inhibitor) and cPTIO (NO scavenger) decreased the S-nitrosothiol (SNO) contents, which was followed by the increased expression of NO-synthesis-related-genes by MT + NO. Interestingly, MT + NO-induced drought stress tolerance was coupled with increased expression of transcription factors such as GmWRKY27 and GmMYB174. Conclusively, the physiological, antioxidant, and molecular analysis showed that MT triggers downregulated NO accumulation, promoting tolerance against drought stress.

  • 14.
    Imran, Qari Muhammad
    et al.
    Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Falak, Noreen
    Hussain, Adil
    Mun, Bong-Gyu
    Sharma, Arti
    Lee, Sang-Uk
    Kim, Kyung-Min
    Yun, Byung-Wook
    Nitric oxide responsive heavy metal-associated gene AtHMAD1 contributes to development and disease resistance in Arabidopsis thaliana2016Inngår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, artikkel-id 712Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis. Of those 14 genes, the expression of eight HMA genes was significantly increased, whereas that of six genes was significantly reduced. We further validated the RNA-seq results through quantitative real-time PCR analysis. Gene ontology analysis revealed the involvement of these genes in biological processes such as hemostasis and transport. The majority of these nitric oxide (NO)-responsive AtHMA gene products are carrier/transport proteins. AtHMAD1 (At1g51090) showed the highest fold change to S-nitrosocystein. We therefore, further investigated its role in oxidative and nitrosative mediated stress conditions and found that AtHMAD1 has antagonistic role in shoot and root growth. Characterization of AtHMAD1 through functional genomics showed that the knock out mutant athmad1 plants were resistant to virulent Pseudomonas syringae (DC3000) and showed early induction and high transcript accumulation of pathogenesis related gene. Furthermore, inoculation of athamd1 with avirulent strain of the same bacteria showed negative regulation of R-gene mediated resistance. These results were supported by hypersensitive cell death response and cell death induced electrolyte leakage. AtHMAD1 was also observed to negatively regulate systemic acquired resistance SAR as the KO mutant showed induction of SAR marker genes. Overall, these results imply that NO-responsive AtHMA domain containing genes may play an important role in plant development and immunity.

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  • 15.
    Imran, Qari Muhammad
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik. School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Falak, Noreen
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Hussain, Adil
    Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan.
    Mun, Bong-Gyu
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Yun, Byung-Wook
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Abiotic stress in plants, stress perception to molecular response and role of biotechnological tools in stress resistance2021Inngår i: Agronomy, E-ISSN 2073-4395, Vol. 11, nr 8, artikkel-id 1579Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plants, due to their sessile nature, face several environmental adversities. Abiotic stresses such as heat, cold, drought, heavy metals, and salinity are serious threats to plant production and yield. To cope with these stresses, plants have developed sophisticated mechanisms to avoid or resist stress conditions. A proper response to abiotic stress depends primarily on how plants perceive the stress signal, which in turn leads to initiation of signaling cascades and induction of resistance genes. New biotechnological tools such as RNA-seq and CRISPR-cas9 are quite useful in identifying target genes on a global scale, manipulating these genes to achieve tolerance, and helping breeders to develop stress-tolerant cultivars. In this review, we will briefly discuss the adverse effects of key abiotic stresses such as cold, heat, drought, and salinity. We will also discuss how plants sense various stresses and the importance of biotechnological tools in the development of stress-tolerant cultivars.

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  • 16.
    Imran, Qari Muhammad
    et al.
    Laboratory of Plant Functional Genomics, School of Applied BioSciences, Kyungpook National University, Daegu, Republic of Korea.
    Hussain, Adil
    Lee, Sang-Uk
    Mun, Bong-Gyu
    Falak, Noreen
    Loake, Gary J.
    Yun, Byung-Wook
    Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes2018Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 8, artikkel-id 771Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    TFs are important proteins regulating plant responses during environmental stresses. These insults typically induce changes in cellular redox tone driven in part by promoting the production of reactive nitrogen species (RNS). The main source of these RNS is nitric oxide (NO), which serves as a signalling molecule, eliciting defence and resistance responses. To understand how these signalling molecules regulate key biological processes, we performed a large scale S-nitrosocysteine (CySNO)-mediated RNA-seq analysis. The DEGs were analysed to identify potential regulatory TFs. We found a total of 673 (up- and down-regulated) TFs representing a broad range of TF families. GO-enrichment and MapMan analysis suggests that more than 98% of TFs were mapped to the Arabidopsis thaliana genome and classified into pathways like hormone signalling, protein degradation, development, biotic and abiotic stress, etc. A functional analysis of three randomly selected TFs, DDF1RAP2.6, and AtMYB48 identified a regulatory role in plant growth and immunity. Loss-of-function mutations within DDF1 and RAP2.6 showed compromised basal defence and effector triggered immunity, suggesting their positive role in two major plant defence systems. Together, these results imply an important data representing NO-responsive TFs that will help in exploring the core mechanisms involved in biological processes in plants.

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  • 17.
    Imran, Qari Muhammad
    et al.
    Laboratory of Plant Functional Genomics School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
    Hussain, Adil
    Mun, Bong-Gyu
    Lee, Sang Uk
    Asaf, Sajjad
    Ali, Muhammad Amjad
    Lee, In-Jung
    Yun, Byung-Wook
    Transcriptome wide identification and characterization of NO-responsive WRKY transcription factors in Arabidopsis thaliana L.2018Inngår i: Environmental and Experimental Botany, ISSN 0098-8472, E-ISSN 1873-7307, Vol. 148, s. 128-143Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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 Arabidopsis thaliana, 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 cis-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 in vivo analysis using atwrky62 loss of function mutant and the results indicated a negative role of AtWRKY62 in plant growth. Furthermore, atwrky62 showed significantly less SNO contents compared to wild type plants indicating putative role of AtWRKY62 in NO metabolism.

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  • 18. Imran, Qari Muhammad
    et al.
    Lee, Sang-Uk
    Mun, Bong-Gyu
    Hussain, Adil
    Asaf, Sajjad
    Lee, In-Jung
    Yun, Byung-Wook
    WRKYs, the Jack-of-various-Trades, Modulate Dehydration Stress in Populus davidiana-A Transcriptomic Approach2019Inngår i: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 20, nr 2Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Populus davidiana, native to Korea and central Asian countries, is a major contributor to the Korean forest cover. In the current study, using high-throughput RNA-seq mediated transcriptome analysis, we identified about 87 P. davidiana WRKY transcription factors (PopdaWRKY TFs) that showed differential expression to dehydration stress in both sensitive and tolerant cultivars. Our results suggested that, on average, most of the WRKY genes were upregulated in tolerant cultivars but downregulated in sensitive cultivars. Based on protein sequence alignment, P. davidiana WRKYs were classified into three major groups, I, II, III, and further subgroups. Phylogenetic analysis showed that WRKY TFs and their orthologs in Arabidopsis and rice were clustered together in the same subgroups, suggesting similar functions across species. Significant correlation was found among qRT-PCR and RNA-seq analysis. In vivo analysis using model plant Arabidopsis showed that atwrky62 (orthologous to Potri.016G137900) knockout mutants were significantly sensitive to dehydration possibly due to an inability to close their stomata under dehydration conditions. In addition, a concomitant decrease in expression of ABA biosynthetic genes was observed. The AtHK1 that regulates stomatal movement was also downregulated in atwrky62 compared to the wild type. Taken together, our findings suggest a regulatory role of PopdaWRKYs under dehydration stress.

  • 19.
    Imran, Qari Muhammad
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik. School of Applied Biosciences, Kyungpook National University, Buk-gu, Daegu, South Korea.
    Shahid, Muhammad
    School of Applied Biosciences, Kyungpook National University, Buk-gu, Daegu, South Korea; Agriculture Research Institute, Khyber Pakhtunkhwa, Mingora, Pakistan.
    Hussain, Adil
    Department of Agriculture, Abdul Wali Khan University, Khyber Pakhtunkhwa, Mardan, Pakistan.
    Yun, Byung-Wook
    School of Applied Biosciences, Kyungpook National University, Buk-gu, Daegu, South Korea.
    NO and ROS crosstalk and acquisition of abiotic stress tolerance2021Inngår i: Nitric oxide in plant biology: an ancient molecule with emerging roles / [ed] Vijay Pratap Singh; Samiksha Singh; Durgesh Kumar Tripathi; Maria C. Romero-Puertas; Luisa Maria Sandalio, Elsevier, 2021, s. 477-491Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Nitric oxide (NO) and H2O2, known as signaling molecules, particularly regulate various cellular processes under stress conditions. Abiotic stress, like other stresses, leads to the production of reactive oxygen and nitrogen species (ROS and RNS, respectively). The interaction or crosstalk between these two redox molecules is important for the regulation of cellular processes. Increasing evidence has suggested that NO transfers its bioactivity through posttranslational modifications, the major among them is S-nitrosation, the covalent attachment of an NO moiety to a cysteine thiol that can bring conformational changes in proteins and hence in their functions. S-nitrosation of the tripeptide glutathione (GSH) results in the formation of S-nitrosoglutathione (GSNO), which is a relatively stable reservoir of NO. The formation of GSNO, therefore, determines cellular redox status, crucial for normal metabolic activities, and is regulated by key enzyme GSNO reductase (GSNOR) in plants. Here, we overview the importance of H2O2 and NO as signaling molecules in plants and their roles in stress tolerance. We also discuss crosstalk between H2O2 and NO and its importance in abiotic stress tolerance, with examples of salt, cold, drought, metal, and heat tolerance. The accumulated data from the cited research has important implications for the improved productivity of many crop plants.

  • 20. Imran, Qari Muhammad
    et al.
    Yun, Byung-Wook
    Pathogen-induced Defense Strategies in Plants2020Inngår i: Journal of Crop Science and Biotechnology, Vol. 23, nr 2, s. 97-105Artikkel i tidsskrift (Fagfellevurdert)
  • 21. Kamran, Muhammad
    et al.
    Imran, Qari Muhammad
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik. Laboratory of Plant Molecular Pathology and Functional Genomics, Division of Plant Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, South Korea.
    Ahmed, Muhammad Bilal
    Falak, Noreen
    Khatoon, Amna
    Yun, Byung-Wook
    Endophyte-mediated stress tolerance in plants: a sustainable strategy to enhance resilience and assist crop improvement2022Inngår i: Cells, E-ISSN 2073-4409, Vol. 11, nr 20, artikkel-id 3292Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Biotic and abiotic stresses severely affect agriculture by affecting crop productivity, soil fertility, and health. These stresses may have significant financial repercussions, necessitating a practical, cost-effective, and ecologically friendly approach to lessen their negative impacts on plants. Several agrochemicals, such as fertilizers, pesticides, and insecticides, are used to improve plant health and protection; however, these chemical supplements have serious implications for human health. Plants being sessile cannot move or escape to avoid stress. Therefore, they have evolved to develop highly beneficial interactions with endophytes. The targeted use of beneficial plant endophytes and their role in combating biotic and abiotic stresses are gaining attention. Therefore, it is important to experimentally validate these interactions and determine how they affect plant fitness. This review highlights research that sheds light on how endophytes help plants tolerate biotic and abiotic stresses through plant–symbiont and plant–microbiota interactions. There is a great need to focus research efforts on this vital area to achieve a system-level understanding of plant–microbe interactions that occur naturally.

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  • 22. Kamran, Muhammad
    et al.
    Khan, Abdul L.
    Ali, Liaqat
    Hussain, Javid
    Waqas, Muhammad
    Al-Harrasi, Ahmed
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Kim, Yoon-Ha
    Kang, Sang-Mo
    Yun, Byung-Wook
    Hydroquinone; a novel bioactive compound from plant-derived smoke can cue seed germination of lettuce2017Inngår i: Frontiers in Chemistry, E-ISSN 2296-2646, Vol. 5, artikkel-id 30Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plant-derived smoke has been known to play an important role in distribution and growth of vegetation. Using a proficiently designed furnace, we extracted smoke from the leaves of four plant viz. Helianthus annuus,Aloe vera,Ginkgo biloba, and Cymbopogon jwarancusa. Smoke dilutions obtained from these plants were obtained in different concentrations to identify potential lettuce growth promoting smoke solution. Results revealed that smoke obtained from G. biloba significantly enhanced the lettuce seed germination. This solution was then partitioned into ethyl acetate, dichloromethane, n-hexane, chloroform and ether fractions. Ethyl acetate fraction was found to be potent to enhance seed germination. This fraction was subjected to column chromatography and spectroscopic techniques to obtain compound 1. This compound was identified as hydroquinone using 1D and 2D NMR techniques. At low concentrations (5, 10, and 20 ppm), compound 1 enhanced the lettuce seed germination; however, higher concentrations inhibited its growth as compared to control.

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  • 23. Khan, Abdul Latif
    et al.
    Al-Harrasi, Ahmed
    Shahzad, Raheem
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
    Yun, Byung-Wook
    Kim, Yoon-Ha
    Kang, Sang-Mo
    Al-Rawahi, Ahmed
    Lee, In-Jung
    Regulation of endogenous phytohormones and essential metabolites in frankincense-producing Boswellia sacra under wounding stress2018Inngår i: Acta Physiologiae Plantarum, ISSN 0137-5881, E-ISSN 1861-1664, Vol. 40, nr 6, artikkel-id 113Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Boswellia sacra is an economically and ecologically important frankincense-producing tree, which is wounded to extract the aromatic resin. However, the underlying physiological mechanisms following this wounding stress are unknown. Our current goal was to elucidate the regulation of key physio-molecular determinants of wounded and preserved B. sacra populations. Wounding caused a twofold increase in calcium/magnesium content and a reduction in essential macronutrient (nitrogen) levels. Total amino acids were also reduced 1.74-fold; however, the levels of γ-amino butyric acid, hydroxyl-proline, and β-alanine were significantly higher (1- to 2.2-fold). In contrast, the fatty acids (linolenic, palmitic, stearic, and linoleic acids) were significantly higher in the preserved trees. Endogenous jasmonic acid (JA) was also significantly higher (67%) in the wounded trees, as was the expression of the JA-related genes allene oxide synthase and allene oxide cyclase. A similar twofold increase in stress-responsive abscisic acid was observed in the wounded trees. However, salicylic acid was down-regulated, and the pathogenesis-related genes PR1 and PR3 exhibited varying responses in the wounded plants. The presence of physiologically active (GA1, GA4, and GA3) and inactive (GA12, GA19, and GA20) gibberellins in both the wounded and control trees revealed similarity with the known GA biosynthesis in B. sacra. Both GA4 and GA3 were each significantly synthesized, which were buoyed by the increased expressions of ent-copalyl diphosphate synthase, cytochrome P450 monooxygenases, and gibberellin 20 oxidases under wounding stress. In conclusion, B. sacra responds to extraction of resin by regulating essential endogenous hormones and related transcripts, which in return retard tree growth and development.

  • 24. Khan, Murtaza
    et al.
    Imran, Qari Muhammad
    Shahid, Muhammad
    Mun, Bong-Gyu
    Yun, Byung-Wook
    Nitric oxide-induced AtAO3 differentially regulates plant defense against Pseudomonas syringae pv. tomato in Arabidopsis thaliana2019Inngår i: BMC Plant Biology, E-ISSN 1471-2229, artikkel-id 602Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Exposure of plants to different environmental insults instigates significant changes in the cellular redox tone driven in part by promoting the production of reactive nitrogen species. The key player, nitric oxide (NO) is a small gaseous diatomic molecule, well-known for its signaling role during stress. In this study, we focused on abscisic acid (ABA) metabolism-related genes that showed differential expression in response to the NO donor S-nitroso-L-cysteine (CySNO) by conducting RNA-seq-based transcriptomic analysis.

    Results: CySNO-induced ABA-related genes were identified and further characterized. Gene ontology terms for biological processes showed most of the genes were associated with protein phosphorylation. Promoter analysis suggested that several cis-regulatory elements were activated under biotic and/or abiotic stress conditions. The ABA biosynthetic gene AtAO3 was selected for validation using functional genomics. The loss of function mutant atao3 was found to differentially regulate oxidative and nitrosative stress. Further investigations for determining the role of AtAO3 in plant defense suggested a negative regulation of plant basal defense and R-gene-mediated resistance. The atao3 plants showed resistance to virulent Pseudomonas syringae pv. tomato strain DC3000 (Pst DC3000) with gradual increase in PR1 gene expression. Similarly, atao3 plants showed increased hypersensitive response (HR) when challenged with Pst DC3000 (avrB). The atgsnor1–3 and atsid2 mutants showed a susceptible phenotype with reduced PR1 transcript accumulation. Drought tolerance assay indicated that atao3 and atnced3 ABA-deficient mutants showed early wilting, followed by plant death. The study of stomatal structure showed that atao3 and atnced3 were unable to close stomata even at 7 days after drought stress. Further, they showed reduced ABA content and increased electrolyte leakage than the wild-type (WT) plants. The quantitative polymerase chain reaction analysis suggested that ABA biosynthesis genes were down-regulated, whereas expression of most of the drought-related genes were up-regulated in atao3 than in WT.

    Conclusions: AtAO3 negatively regulates pathogen-induced salicylic acid pathway, although it is required for drought tolerance, despite the fact that ABA production is not totally dependent on AtAO3, and that drought-related genes like DREB2 and ABI2 show response to drought irrespective of ABA content.

  • 25. Mun, Bong-Gyu
    et al.
    Hussain, Adil
    Park, Eung-Jun
    Lee, Sang-Uk
    Sharma, Arti
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu 701-702, Republic of Korea.
    Jung, Ki-Hong
    Yun, Byung-Wook
    Profile and time-scale dynamics of differentially expressed genes in transcriptome of Populus davidiana under drought stress2017Inngår i: Plant Molecular Biology Reporter, ISSN 0735-9640, E-ISSN 1572-9818, Vol. 35, nr 6, s. 647-660Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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 Pdavidiana in response to drought stress, providing critical information necessary for understanding the mechanisms underpinning drought stress tolerance in forest trees and other plant species.

  • 26. Mun, Bong-Gyu
    et al.
    Lee, Sang-Uk
    Park, Eung-Jun
    Kim, Hyun-Ho
    Hussain, Adil
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.
    Lee, In-Jung
    Yun, Byung-Wook
    Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana2017Inngår i: 3 Biotech, E-ISSN 2190-5738, Vol. 7, artikkel-id 209Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana 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 P. trichocarpa 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 (R = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was P. davidiana specific. The sequence of P. davidiana ortholog of P. trichocarpa 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 P. trichocarpa 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 P. davidiana-specific POPTR_0018s10230 is different at six different positions compared to P. trichocarpa, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in P. davidiana 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.

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  • 27. Nabi, Rizwana Begum Syed
    et al.
    Tayade, Rupesh
    Hussain, Adil
    Kulkarni, Krishnanand P
    Imran, Qari Muhammad
    Mun, Bong-Gyu
    Yun, Byung-Wook
    Nitric oxide regulates plant responses to drought, salinity, and heavy metal stress2019Inngår i: Environmental and Experimental Botany, ISSN 0098-8472, E-ISSN 1873-7307, Vol. 161, s. 120-133Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plants are exposed to diverse abiotic stresses like drought, heat, salinity, and high-metal concentrations at different stages of their life cycle. As protection against stress, plants release signaling molecules that initiate a cascade of stress-adaptation responses leading either to programmed cell death or plant acclimation. Nitric oxide (NO) is a small but important redox signaling molecule that in plants is involved in a diverse range of physiological processes including germination, development, flowering, senescence, and abiotic stress. Although the exact role of NO in plants remains unclear and is species dependent, various studies have suggested a positive correlation between NO accumulations in stress in plants. In this article, we review and discuss the biosynthesis of NO, sources and exogenous application of NO donors under drought, salt, and heavy metal stress. A review of publications indicated that, in general, application of exogenous NO alleviates the negative stress effects in plants and improves antioxidant activity in most plant species. In addition, S-nitrosylation and tyrosine nitration are two NO-mediated posttranslational modification. All these factors are important in protecting plants from diverse stresses and vary with the species. Furthermore, to determine precise mechanisms of action of NO is expected to help in efficient utilization of crop cultivation under stress conditions.

  • 28. Nabi, Rizwana Begum Syed
    et al.
    Tayade, Rupesh
    Imran, Qari Muhammad
    Hussain, Adil
    Shahid, Muhammad
    Yun, Byung-Wook
    Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana2020Inngår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11Artikkel i tidsskrift (Fagfellevurdert)
  • 29. Shahid, Muhammad
    et al.
    Imran, Qari Muhammad
    Hussain, Adil
    Khan, Murtaza
    Lee, Sang Uk
    Mun, Bong Gyu
    Yun, Byung-Wook
    Comprehensive Analyses of Nitric Oxide-Induced Plant Stem Cell-Related Genes in Arabidopsis thaliana2019Inngår i: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, nr 3, artikkel-id 190Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plant stem cells are pluripotent cells that have diverse applications in regenerative biology and medicine. However, their roles in plant growth and disease resistance are often overlooked. Using high-throughput RNA-seq data, we identified approximately 20 stem cell-related differentially expressed genes (DEGs) that were responsive to the nitric oxide (NO) donor S-nitrosocysteine (CySNO) after six hours of infiltration. Among these DEGs, the highest number of positive correlations (R ≥ 0.8) was observed for CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) 12. Gene ontology (GO) terms for molecular function showed DEGs associated with signal transduction and receptor activity. A promoter study of these DEGs showed the presence of cis-acting elements that are involved in growth as well as the regulation of abiotic and biotic stress. Phylogenetic analysis of the Arabidopsis stem cell-related genes and their common orthologs in rice, soybean, poplar, and tomato suggested that most soybean stem cell-related genes were grouped with the Arabidopsis CLE type of stem cell genes, while the rice stem cell-related genes were grouped with the Arabidopsis receptor-like proteins. The functional genomic-based characterization of the role of stem cell DEGs showed that under control conditions, the clv1 mutant showed a similar phenotype to that of the wild-type (WT) plants; however, under CySNO-mediated nitrosative stress, clv1 showed increased shoot and root length compared to WT. Furthermore, the inoculation of clv1 with virulent Pst DC3000 showed a resistant phenotype with fewer pathogens growing at early time points. The qRT-PCR validation and correlation with the RNA-seq data showed a Pearson correlation coefficient of >0.8, indicating the significantly high reliability of the RNA-seq analysis.

  • 30. Sharma, Arti
    et al.
    Hussain, Adil
    Mun, Bong-Gyu
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
    Falak, Noreen
    Lee, Sang-Uk
    Kim, Jae Young
    Hong, Jeum Kyu
    Loake, Gary John
    Ali, Asad
    Comprehensive analysis of plant rapid alkalization factor (RALF) genes2016Inngår i: Plant physiology and biochemistry (Paris), ISSN 0981-9428, E-ISSN 1873-2690, Vol. 106, s. 82-90Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Receptor mediated signal carriers play a critical role in the regulation of plant defense and development. Rapid alkalization factor (RALF) proteins potentially comprise important signaling components which may have a key role in plant biology. The RALF gene family contains large number of genes in several plant species, however, only a few RALF genes have been characterized to date. In this study, an extensive database search identified 39, 43, 34 and 18 RALF genes in Arabidopsis, rice, maize and soybean, respectively. These RALF genes were found to be highly conserved across the 4 plant species. A comprehensive analysis including the chromosomal location, gene structure, subcellular location, conserved motifs, protein structure, protein-ligand interaction and promoter analysis was performed. RALF genes from four plant species were divided into 7 groups based on phylogenetic analysis. In silico expression analysis of these genes, using microarray and EST data, revealed that these genes exhibit a variety of expression patterns. Furthermore, RALF genes showed distinct expression patterns of transcript accumulation in vivo following nitrosative and oxidative stresses in Arabidopsis. Predicted interaction between RALF and heme ligand also showed that RALF proteins may contribute towards transporting or scavenging oxygen moieties. This suggests a possible role for RALF genes during changes in cellular redox status. Collectively, our data provides a valuable resource to prime future research in the role of RALF genes in plant growth and development.

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