Amid apprehension of global climate change, crop plants are inevitably confronted with a myriad of abiotic stress factors during their growth that inflicts a serious threat to their development and overall productivity. These abiotic stresses comprise extreme temperature, pH, high saline soil, and drought stress. Among different abiotic stresses, drought is considered the most calamitous stressor with its serious impact on the crops' yield stability. The development of climate-resilient crops that withstands reduced water availability is a major focus of the scientific fraternity to ensure the food security of the sharply increasing population. Numerous studies aim to recognize the key regulators of molecular and biochemical processes associated with drought stress tolerance response. A few potential candidates are now considered as promising targets for crop improvement. Transcription factors act as a key regulatory switch controlling the gene expression of diverse biological processes and, eventually, the metabolic processes. Understanding the role and regulation of the transcription factors will facilitate the crop improvement strategies intending to develop and deliver agronomically-superior crops. Therefore, in this review, we have emphasized the molecular avenues of the transcription factors that can be exploited to engineer drought tolerance potential in crop plants. We have discussed the molecular role of several transcription factors, such as basic leucine zipper (bZIP), dehydration responsive element binding (DREB), DNA binding with one finger (DOF), heat shock factor (HSF), MYB, NAC, TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP), and WRKY. We have also highlighted candidate transcription factors that can be used for the development of drought-tolerant crops.

Transcription factors as key molecular target to strengthen the drought stress tolerance in plants.

The DNA binding with one finger (Dof) proteins, a family of plant-specific transcription factors, are involved in a variety of plant biological processes. However, little information is available on their involvement in fruit ripening. We have characterized 25 MaDof genes from banana fruit (Musa acuminata), designated as MaDof1-MaDof25 Gene expression analysis in fruit subjected to different ripening conditions revealed that MaDofs were differentially expressed during different stages of ripening. MaDof10, 23, 24, and 25 were ethylene-inducible and nuclear-localized, and their transcript levels increased during fruit ripening. Moreover, yeast two-hybrid and bimolecular fluorescence complementation analyses demonstrated a physical interaction between MaDof23 and MaERF9, a potential regulator of fruit ripening reported in a previous study. We determined that MaDof23 is a transcriptional repressor, whereas MaERF9 is a transcriptional activator. We suggest that they might act antagonistically in regulating 10 ripening-related genes, including MaEXP1/2/3/5, MaXET7, MaPG1, MaPME3, MaPL2, MaCAT, and MaPDC, which are associated with cell wall degradation and aroma formation. Taken together, our findings provide new insight into the transcriptional regulation network controlling banana fruit ripening.

/pdf/the-banana-fruit-dof-transcription-factor-madof23-acts-as-a-1ukdtnxv8j.pdf

The banana fruit Dof transcription factor MaDof23 acts as a repressor and interacts with MaERF9 in regulating ripening-related genes

The DNA-binding with one zinc finger proteins (Dofs) are a plant-specific family of transcription factors. The Dofs are involved in a variety of biological processes such as phytohormone production, seed development, and environmental adaptation. Dofs have been previously identified in several plants, but not in pepper. We identified 33 putative Dof genes in pepper (CaDofs). To gain an overview of the CaDofs, we analyzed phylogenetic relationships, protein motifs, and evolutionary history. We divided the 33 CaDofs, containing 25 motifs, into four major groups distributed on eight chromosomes. We discovered an expansion of the CaDofs dated to a recent duplication event. Segmental duplication that occurred before the speciation of the Solanaceae lineages was predominant among the CaDofs. The global gene-expression profiling of the CaDofs by RNA-seq analysis showed distinct temporal and pathogen-specific variation during development and response to biotic stresses (two TMV strains, PepMoV, and Phytophthora capsici), suggesting functional diversity among the CaDofs. These results will provide the useful clues into the responses of Dofs in biotic stresses and promote a better understanding of their multiple function in pepper and other species.

/pdf/genome-wide-analysis-of-dof-transcription-factors-reveals-25bca7hmxh.pdf

Genome-wide analysis of Dof transcription factors reveals functional characteristics during development and response to biotic stresses in pepper.

Cucumber is vulnerable to many foliage diseases. Recent studies reported cloning of candidate genes for several diseases in cucumber; however, the exact defence mechanisms remain unclear. Dof genes have been shown to play significant roles in plant growth, development and responses to biotic and abiotic stresses. Dof genes coding for plant-specific transcription factors can promote large-scale expression of defence-related genes at whole genome level. The genes in the family have been identified and characterized in several plant species, but not in cucumber. In the present study, we identified 36 CsDof members from the cucumber draft genomes which could be classified into eight groups. The proportions of the CsDof family genes, duplication events, chromosomal locations, cis-elements and miRNA target sites were comprehensively investigated. Consequently, we analysed the expression patterns of CsDof genes in specific tissues and their response to two biotic stresses (watermelon mosaic virus and downy mildew). These results indicated that CsDof may be involved in resistance to biotic stresses in cucumber.

/pdf/identification-and-characterisation-of-dof-transcription-55mfrokyuu.pdf

Identification and characterisation of Dof transcription factors in the cucumber genome

Genome-wide analysis and expression profiling of DNA-binding with one zinc finger (Dof) transcription factor family in potato

Main conclusion
The structural, functional and in-silico studies of Dof transcription factor attempted so far reveals immense opportunity to analyze the plant genomes in terms of number of Dof genes and discuss in light of the evolution. The multiple functions of Dof genes needs to explored for crop improvement.

Transcription factors play a very vital role in gene regulation at transcriptional level and are being extensively studied across phylas. In recent years, sequencing of plant genomes has led to genome-wide identification and characterizations of diverse types of plant-specific transcription factor gene family providing key insights into their structural and functional diversity. The DNA binding with one finger (Dof), a class belonging to C2H2-type zinc finger family proteins, is a plant-specific transcription factor having multiple roles such as seed maturation and germination, phytohormone and light-mediated regulation and plant responses to biotic and abiotic stresses. Dof proteins are present across plant lineage, from green algae to higher angiosperm, and represent a unique class of transcription factor having bifunctional binding activities, with both DNA and proteins, to regulate the complex transcriptional machinery in plant cells. The structural and functional diversity of the Dof transcription factor family along with the bioinformatics analysis highlighting the phylogeny of Dof families is reviewed in light of its importance in plant biotechnology for crop improvement.

Insights into structural and functional diversity of Dof (DNA binding with one finger) transcription factor

The genome mining of chickpea (Cicer arietinum L.) revealed a total of 37 putative Dof genes using NCBI BLAST search against the genome with a highly conserved Dof domain. The translated Dof proteins possessed 150–493 amino acid residues with molecular weight ranging from 16.9 to 54.4 kD and pI varied from 4.98 to 9.64 as revealed by ExPASy server ProtParam. The exon–intron organization showed predominance of intronless Dof genes in chickpea. The predicted Dof genes were distributed among the eight chromosomes with a maximum of 9 Dof genes present on chromosome 7 and a single Dof gene was found on chromosome 8.The predominance of segmental gene duplication as compared to tandem duplication was observed which might be the prime cause of Dof gene family expansion in chickpea. The cis-regulatory element analysis revealed the presence of light-responsive, hormone-responsive, endosperm-specific, meristem-specific and stress-responsive elements. Comprehensive phylogenetic analyses of Dof genes of chickpea with Arabidopsis, rice, soybean and pigeonpea revealed several orthologs and paralogs assisting in understanding the putative functions of CaDof genes. The functional divergence and site-specific selective pressures of chickpea Dof genes have been investigated. The bioinformatics-based genome-wide assessment of Dof gene family of chickpea attempted in the present study could be a significant step for deciphering novel Dof genes based on genome-wide expression profiling.

Genome-wide bioinformatics analysis of Dof transcription factor gene family of chickpea and its comparative phylogenetic assessment with Arabidopsis and rice

The polygalacturonases (PG) is one of the important members of pectin-degrading glycoside hydrolases of the family GH28. In plants, PG represents multigene families associated with diverse processes. In the present study, an attempt has been made to investigate the diversity of PG genes among monocots and dicots with respect to phylogeny, gene duplication and subcellular localization to get an insight into the evolutionary and functional attributes. The genome-wide assessment of Medicago truncatula, Vitis vinifera Sorghum bicolor, and Oryza sativa L. ssp. japonica genomes revealed 53, 49, 38 and 35 PG-like (PGL) genes, respectively. The predominance of glyco_hydro_28 domain, hydrophilic nature and genes with multiple introns were uniformly observed. The subcellular localization showed the presence of signal sequences targeting the secretory pathways. The phylogenetic tree constructed marked uniformity with three distinct clusters for each plant irrespective of the variability in the genome sizes. The site-specific selection pressure analysis based on K a/K s values showed predominance of purifying selection pressures among different groups identified in these plants. The functional divergence analysis revealed significant site-specific selective constraints. Results of site-specific selective pressure analysis throw light on the functional diversity of PGs in various plant processes and hence its constitutive nature. These findings are further strengthened by functional divergence analysis which reveals functionally diverse groups in all the four species representing monocots and dicots. The outcome of the present work could be utilized for deciphering the novel functions of PGs in plants.

Genome-Wide Assessment of Polygalacturonases-Like (PGL) Genes of Medicago truncatula , Sorghum bicolor , Vitis vinifera and Oryza sativa Using Comparative Genomics Approach

A total of 28 pectate lyase (PL) sequences representing different species of Aspergillus namely A. flavus, A. niger, A. nidulans, A. fumigatus, A. oryzae, A. clavatus and A. terreus were retrieved from NCBI databases and in-silico characterized for structural diversity. The translated amino acids sequences of these PL genes of Aspergillus were also accessed for various physio-chemical features like molecular weight, theoretical PI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).These sequences exhibit multiple introns and revealed a conserved pectate lyases domain irrespective of Aspergillus species, suggesting its possible role in structural and catalytic attributes of PLs. Homology modeling was performed with Swiss-model workspace at automated mode with selected template to predict the 3D structures of PL proteins. The stability of the 3D models were confirmed by PROCHECK showing more than 95% of the amino acid residues in favored and allowed region of Ramachandran plot and also by favorable QMEAN-Z score. The phylogenetic tree constructed revealed four distinct groups which were further subjected for functional divergence studies. The coefficient of functional divergence (Ɵ) among different groups was found to be less than 1 indicating significant site–specific selective constraints. The bioinformatics study of pectate lyases of different species of Aspergillus gives an insight to the structural variability which further needs to be analyzed for functional attributes.

http://www.biosciencejournals.com/archives/2014/vol2issue6/11.1.pdf

Computational assessment of predicted three dimensional structures of Pectate lyases from different species of Aspergillus using homology modeling

http://www.biosciencejournals.com/archives/2014/vol2issue4/4.1.pdf

Jeya Nasim

Papers

Insights into structural and functional diversity of Dof (DNA binding with one finger) transcription factor

Genome-wide bioinformatics analysis of Dof transcription factor gene family of chickpea and its comparative phylogenetic assessment with Arabidopsis and rice

Genome-Wide Assessment of Polygalacturonases-Like (PGL) Genes of Medicago truncatula , Sorghum bicolor , Vitis vinifera and Oryza sativa Using Comparative Genomics Approach

Computational assessment of predicted three dimensional structures of Pectate lyases from different species of Aspergillus using homology modeling

Computational Insights into Three Dimensional Structures of Dof transcription factors of Sorghum bicolor (L) Moench