Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach

Kumar, Anuj; Kumar, Sanjay; Kumar, Upendra; Suravajhala, Prashanth; Gajula, Mnv Prasad

doi:10.1016/j.compbiolchem.2016.07.008

Cited by 27 publications

(13 citation statements)

References 56 publications

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“…All TaRKDs and TaNLPs (except TaRKD3-7s and TaRKD6b-2B) were localized in the nucleus providing support for their function as transcription factors (S7 Table) [27]. The functional annotation analysis also suggested their involvement in different activities including DNA binding, metal ion binding, protein binding and ATP binding, thus influencing several biological processes including cellular, metabolic and biosynthetic processes (S5 Fig).…”

Section: Resultsmentioning

confidence: 89%

“…78.3% in TaRKD9-3A to 96.3% in TaRKD6-2A; 75.9% in TaNLP5-6A to 84.7% in TaNLP3-4A) suggesting satisfactory geometry of the predicted 3D structures (S5 Table). The use of Ramachandran plot for evaluation of the accuracy of protein structures is known and has been emphasized in several recent studies [27, 66]. The 3D structures of TaRKDs and TaNLPs have been submitted to Protein Model Database (PMDB) (https://bioinformatics.cineca.it/PMDB/) [67], which can be freely accessed (S5 Table).…”

Section: Resultsmentioning

confidence: 99%

“…Both 3D protein and nitrate complexes had at least 5Å buffer in every direction of the box to permit substantial fluctuations of the conformation during the course of the MD simulation. The complete interaction energy was also calculated [27,28]. The constant pressure during MD simulation was calculated using anisotropic diagonal position scaling.…”

Section: Methodsmentioning

confidence: 99%

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Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.)

et al. 2018

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RWP-RKs represent a small family of transcription factors (TFs) that are unique to plants and function particularly under conditions of nitrogen starvation. These RWP-RKs have been classified in two sub-families, NLPs (NIN-like proteins) and RKDs (RWP-RK domain proteins). NLPs regulate tissue-specific expression of genes involved in nitrogen use efficiency (NUE) and RKDs regulate expression of genes involved in gametogenesis/embryogenesis. During the present study, using in silico approach, 37 wheat RWP-RK genes were identified, which included 18 TaNLPs (2865 to 7340 bp with 4/5 exons), distributed on 15 chromosomes from 5 homoeologous groups (with two genes each on 4B,4D and 5A) and 19 TaRKDs (1064 to 5768 bp with 1 to 6 exons) distributed on 12 chromosomes from 4 homoeologous groups (except groups 1, 4 and 5); 2–3 splice variants were also available in 9 of the 37 genes. Sixteen (16) of these genes also carried 24 SSRs (simple sequence repeats), while 11 genes had targets for 13 different miRNAs. At the protein level, MD simulation analysis suggested their interaction with nitrate-ions. Significant differences were observed in the expression of only two (TaNLP1 and TaNLP2) of the nine representative genes that were used for in silico expression analysis under varying levels of N at post-anthesis stage (data for other genes was not available for in silico expression analysis). Differences in expression were also observed during qRT-PCR, when expression of four representative genes (TaNLP2, TaNLP7, TaRKD6 and TaRKD9) was examined in roots and shoots of seedlings (under different conditions of N supply) in two contrasting genotypes which differed in NUE (C306 with low NUE and HUW468 with high NUE). These four genes for qRT-PCR were selected on the basis of previous literature, level of homology and the level of expression (in silico study). In particular, the TaNLP7 gene showed significant up-regulation in the roots and shoots of HUW468 (with higher NUE) during N-starvation; this gene has already been characterized in Arabidopsis and tobacco, and is known to be involved in nitrate-signal transduction pathway.

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Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.)

et al. 2018

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“…In order to conduct the similarity searches BLASTP algorithm was performed against wheat genome assembly TGACv1 publically available on EnsemblPlants platform (Bolser et al, 2016). The results of BLAST analysis were used to identify 'putative' wheat ortholog using the criteria followed by Kumar et al, (2016aKumar et al, ( , 2016b, Nagaraju et al, (2018), Supriya et al, (2018), Mathpal et al, (2018). Conserved domain search (CD-Search) program was used to predict functional domain inside the protein sequence of OsENOD93-1 and its wheat ortholog TaENOD93-1 (Marchler-Bauer et al, 2017).…”

Section: In-silico Chromosomal Mapping Of Taendo93-1 In Wheat Genomementioning

confidence: 99%

Identification and Functional Characterization an Ortholog of OsENOD93-1 Gene in Wheat Using in-silico Approach

Kumar¹,

Kumar²,

Tyagi³

et al. 2018

Int.J.Curr.Microbiol.App.Sci

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Nitrogen is an essential macromolecule necessary for suitable growth and development of plants by playing a vital role in biochemical and physiological functions throughout the life cycle. Early node 93 (ENOD93-1) gene is well known for significantly responding to both N induction and N reduction in plants, but little is known about the structure and function of the ENOD93-1 protein in cereal crops. In this study, a putative ortholog of rice OsENOD93-1 gene was identified in the wheat genome. BLASTP analysis showed the OsENOD93-1 shared the 80% similarity with wheat TRIAE_CS42_4AL_TGACv1_ 288261_AA0942630.1 scaffold. Present study describes the location of TaENOD93-1 gene on4AL chromosome of wheat. MicroRNA target analysis revealed that TaENOD93-1 gene targeting by miR6201. Phylogeny tree suggested that identified putative ortholog shared the evolutionary relationship with monocots. The three dimensional structure of TaENOD93-1 protein was predicted using computer-aided molecular modeling technique followed by structure evaluation using Ramachandran plot. The primary goal of this study was to mapping the chromosomal location and functional annotation of TaENOD93-1 gene in wheat using bioinformatics approach. The identification of putative ortholog of OsENOD93-1 gene in wheat has opened up new opportunities to improve the nitrogen use efficiency (NUE) in wheat through molecular breeding approach. K e y w o r d s

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“…Due to generation and availability of huge genomic information online of the crop plants, the computational studies i.e. performed on computer or via computer simulation are important areas of interest for genomics researchers for comparative genomics study [31,21,15].…”

Section: Introductionmentioning

confidence: 99%

Computational Identification of Conserved Domains from Genomic Survey Sequences in Green Gram [Vigna radiata (L.) R. Wilczek]

Eruvuri¹

2017

IJHA

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Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach

Cited by 27 publications

References 56 publications

Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.)

Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.)

Identification and Functional Characterization an Ortholog of OsENOD93-1 Gene in Wheat Using in-silico Approach

Computational Identification of Conserved Domains from Genomic Survey Sequences in Green Gram [Vigna radiata (L.) R. Wilczek]

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