Genome wide analysis of stress responsive WRKY transcription factors in Arabidopsis thaliana

Sultan, Shaiq; Ali, Muhammad Amjid; Atif, Rana Muhammad; Azeem, Farrukh; Nadeem, Habibullah; Siddique, Muhammad Hussnain; Filiz, Ertuğrul; Hussain, Khadim; Abbas, Amjad

doi:10.24925/turjaf.v4i4.279-290.580

Cited by 4 publications

(4 citation statements)

References 38 publications

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“…It was further determined that both the species share the same evolutionary origin. Our results showed the same pattern as of the distribution of Trithorax homolog genes in chickpea (Qasim et al 2018), WRKY TFs in Arabidopsis (Sultan et al 2016), Potassium transporter genes in chickpea (Azeem et al 2018) and WRKY TFs in chickpea (Waqas et al 2019).…”

Section: Discussionsupporting

confidence: 80%

Comparative Genomics and Expression Analysis of KCS Genes Under Drought Stress in Sunflower (Helianthus Annuus L.)

2022

THE JAPS

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Water stress is considered as the main environmental factor which badly affects growth of sunflower plant. It is a water sensitive plant whose yield is greatly affected by drought stress. Several studies have been done to understand the mechanism of drought stress tolerance in plants, and exploring the role of stress tolerant genes is one of them. KCS genes, responsible for wax biosynthesis, have been reported to be involved in drought stress tolerance mechanism. In this study, expression profiling of KCS genes was done to understand their role in stress mechanism. Comparative genomics studies of KCS genes were carried out in sunflower and Arabidopsis by constructing phylogenetic tree. They were divided into six clades, however they were present in the same clade showing similarities between Arabidopsis and sunflower. It was further confirmed by Synteny analysis and concluded that KCS genes in both species share the same evolutionary origin. Further, they were amplified in sunflower by using gene specific primers. Five genes, i.e. KCS2, KCS4, KCS5, KCS10 and KCS18 were successfully amplified in sunflower variety FH-593. Then, sunflower plants were subjected to drought stress and expression profiling of amplified KCS genes was carried out by Real Time PCR. All the five genes were up-regulated under drought showing their role in stress conditions; however, the expression level of each gene was varied. Maximum relative expression was found for KCS4 gene in T1, i.e. 19 fold as compared to control. The expression of other genes was found in decreasing order as indicated KCS4>KCS2>KCS5>KCS10>KCS18 (relative expression: 19, 12, 5, 4 and 3 respectively). Biochemical analyses were also performed and significant variation was found among treatments and control. Total chlorophyll contents were decreased under drought stress while antioxidants like catalase, peroxidase, superoxide dismutase and proline were increased. Our results showed the role of KCS genes in drought stress which is first ever report in sunflower. This study concluded that KCS genes have role in drought stress tolerance and their expression is significantly up-regulated under stress conditions. The information presented here may help to further characterize KCS genes and their subsequent use to engineer drought stress in crop plants.

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Section: Discussionsupporting

confidence: 80%

Comparative Genomics and Expression Analysis of KCS Genes Under Drought Stress in Sunflower (Helianthus Annuus L.)

2022

THE JAPS

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“…Interestingly, this type of mutation also occurred in the genome of Populus trichocarpa , O. sativa and A . thaliana [32,33,34]. We identified a CX 4 CX 22-23 HXH zinc finger motif in the N-terminal of subgroup I genes, a CX 4 CX 23 HXH motif in the C-terminal of subgroup I genes and II c genes, a CX 5 CX 23 HXH motif in II a, II b, II d and II e genes, and a CX 7 CX 23 HXC motif in subgroup III genes (Figure 4).…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Analysis of Members of the WRKY Gene Family and Their Cold Stress Response in Prunus mume

Bao

Ding

Cheng

et al. 2019

Genes

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Prunus mume, which is a rosaceous arbor with very high ornamental, edible and medical values, has a distribution that is mainly restricted by low temperature. WRKY transcription factor genes play crucial roles in the growth, development, and stress responses of plants. However, the WRKY gene family has not been characterised in P. mume. There were 58 PmWRKYs identified from genome of P. mume. They were anchored onto eight link groups and categorised into three broad groups. The gene structure and motif composition were reasonably conservative in each group. Investigation of gene duplication indicated that nine and seven PmWRKYs were arranged in tandem and segmental duplications, respectively. PmWRKYs were discriminately expressed in different tissues (i.e., roots, stems, leaves, flowers and fruits) in P. mume. The 17 cold-related candidate genes were selected based on RNA-seq data. Further, to investigate the function of PmWRKYs in low temperatures, the expression patterns under artificial cold treatments were analysed. The results showed that the expression levels of the 12 PmWRKYs genes significantly and 5 genes slightly changed in stems. In particular, the expression level of PmWRKY18 was up-regulated after ABA treatment. In addition, the spatiotemporal expression patterns of 17 PmWRKYs were analysed in winter. These results indicated that 17 PmWRKYs were potential transcription factors regulating cold resistance in P. mume.

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“…The structural characteristics of WRKY TFs at the N-terminal and C-terminal determine their binding to W-box (TTGACC/T) or sugar-responsive cis-element (SURE) cis-acting elements in the specific gene promoters (Chuanxin et al, 2003;Ciolkowski et al, 2008;Rushton et al, 1995). In Arabidopsis thaliana (A. thaliana), 72 Arabidopsis thaliana WRKY (AtWRKY ) members were grouped into Group I, II and III because of the difference in the amount of conserved domains and zinc finger structures (Sultan et al, 2016). The members in Group I have a WRKY conserved region at the C-terminal and N-terminal, respectively, and their zinc finger structure is C2-H2 (Eulgem et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development

Sun

Chen

et al. 2020

PeerJ

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Background The WRKY gene family plays important roles in plant biological functions and has been identified in many plant species. With the publication of the Tartary buckwheat genome, the evolutionary characteristics of the WRKY gene family can be systematically explored and the functions of Fagopyrum tataricum WRKY (FtWRKY) genes in the growth and development of this plant also can be predicted. Methods In this study, the FtWRKY genes were identified by the BLASTP method, and HMMER, SMART, Pfam and InterPro were used to determine whether the FtWRKY genes contained conserved domains. The phylogenetic trees including FtWRKY and WRKY genes in other plants were constructed by the neighbor-joining (NJ) and maximum likelihood (ML) methods. The intron and exon structures of the FtWRKY genes were analyzed by the gene structure display server, and the motif compositions were analyzed by MEME. Chromosome location information of FtWRKY genes was obtained with gff files and sequencing files, and visualized by Circos, and the collinear relationship was analyzed by Dual synteny plotter software. The expression levels of 26 FtWRKY genes from different groups in roots, leaves, flowers, stems and fruits at the green fruit, discoloration and initial maturity stage were measured through quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Results A total of 76 FtWRKY genes identified from the Tartary buckwheat genome were divided into three groups. FtWRKY genes in the same group had similar gene structures and motif compositions. Despite the lack of tandem-duplicated gene pairs, there were 23 pairs of segmental-duplicated gene pairs. The synteny gene pairs of FtWRKY genes and Glycine max WRKY genes were the most. FtWRKY42 was highly expressed in roots and may perform similar functions as its homologous gene AtWRKY75, playing a role in lateral root and hairy root formation. FtWRKY9, FtWRKY42 and FtWRKY60 were highly expressed in fruits and may play an important role in fruit development. Conclusion We have identified several candidate FtWRKY genes that may perform critical functions in the development of Tartary buckwheat root and fruit, which need be verified through further research. Our study provides useful information on WRKY genes in regulating growth and development and establishes a foundation for screening WRKY genes to improve Tartary buckwheat quality.

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Genome wide analysis of stress responsive WRKY transcription factors in Arabidopsis thaliana

Cited by 4 publications

References 38 publications

Comparative Genomics and Expression Analysis of KCS Genes Under Drought Stress in Sunflower (Helianthus Annuus L.)

Comparative Genomics and Expression Analysis of KCS Genes Under Drought Stress in Sunflower (Helianthus Annuus L.)

Genome-Wide Analysis of Members of the WRKY Gene Family and Their Cold Stress Response in Prunus mume

Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development

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