In silico study of the CESA and CSL gene family in Arabidopsis thaliana and Oryza sativa: Focus on post-translation modifications

Heidari, Parviz; Ahmadizadeh, Mostafa; Izanlo, Fatemeh; Nußbaumer, Thomas

doi:10.1016/j.plgene.2019.100189

Cited by 42 publications

(36 citation statements)

References 81 publications

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“…In the current study, some conserved motifs in TtAP2/ERF proteins were predicted to lie in the regions outside the DNA-binding domain; moreover, it should be mentioned that both the factors affecting transcriptional modification and nuclear localization-related domains can be found in these regions [75]. The predicted similarity in motif structures may result from recent segregation events across the durum wheat genome and its evolutionary process [76]. Some close association of TtAP2/ERF subfamily members, especially DRF, DREB, and RAV members, with their related counterparts from the Arabidopsis and rice genomes may reveal remarkable similarity in terms of expression and regulatory functions [19].…”

Section: Discussionmentioning

confidence: 65%

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

Faraji

Filiz

Kazemitabar

et al. 2020

Genes

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Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

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Section: Discussionmentioning

confidence: 65%

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

Faraji

Filiz

Kazemitabar

et al. 2020

Genes

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“…The number of introns were variable in tcGASA within genes that cluster together in phylogeny. The loss and gain of introns occurs in the course of evolution within protein-coding genes of the plants and is also reported within the GASA of other plant species (Abdullah et al, 2020a;Ahmad et al, 2019Ahmad et al, , 2020bAhmadizadeh et al, 2020;Ding et al, 2020;Heidari et al, 2019).…”

Section: Discussionmentioning

confidence: 70%

“…However, we also detected four stable proteins: tcGASA3, tcGASA11, tcGASA13, and tcGASA15. The stability demonstrates the lifetime of proteins related to cellular enzymatic reactions (Heidari et al, 2019). Hence, these four proteins may play extensive roles in various enzymatic activities.…”

Section: Discussionmentioning

confidence: 99%

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

Abdullah

Faraji

Mehmood

et al. 2021

Preprint

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The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20–25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.

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“…4 c). CESA3 and CSLG3 are predicted targets of the miRNAs miR838 and miR395, respectively [ 58 , 80 ], which were both identified as up-regulated in dcl234 by the sRNA genome-wide analysis (Figure S 7 B). Together, these results suggest that the ectopic regulation of sRNA homeostasis in dcl234 leads to the reductions in cellulose synthase gene expression and consequently cellulose levels.…”

Section: Resultsmentioning

confidence: 99%

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation

Kaushal

Singh

et al. 2021

Microbiome

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Background Plants are naturally associated with root microbiota, which are microbial communities influential to host fitness. Thus, it is important to understand how plants control root microbiota. Epigenetic factors regulate the readouts of genetic information and consequently many essential biological processes. However, it has been elusive whether RNA-directed DNA methylation (RdDM) affects root microbiota assembly. Results By applying 16S rRNA gene sequencing, we investigated root microbiota of Arabidopsis mutants defective in the canonical RdDM pathway, including dcl234 that harbors triple mutation in the Dicer-like proteins DCL3, DCL2, and DCL4, which produce small RNAs for RdDM. Alpha diversity analysis showed reductions in microbe richness from the soil to roots, reflecting the selectivity of plants on root-associated bacteria. The dcl234 triple mutation significantly decreases the levels of Aeromonadaceae and Pseudomonadaceae, while it increases the abundance of many other bacteria families in the root microbiota. However, mutants of the other examined key players in the canonical RdDM pathway showed similar microbiota as Col-0, indicating that the DCL proteins affect root microbiota in an RdDM-independent manner. Subsequently gene analysis by shotgun sequencing of root microbiome indicated a selective pressure on microbial resistance to plant defense in the dcl234 mutant. Consistent with the altered plant-microbe interactions, dcl234 displayed altered characters, including the mRNA and sRNA transcriptomes that jointly highlighted altered cell wall organization and up-regulated defense, the decreased cellulose and callose deposition in root xylem, and the restructured profile of root exudates that supported the alterations in gene expression and cell wall modifications. Conclusion Our findings demonstrate an important role of the DCL proteins in influencing root microbiota through integrated regulation of plant defense, cell wall compositions, and root exudates. Our results also demonstrate that the canonical RdDM is dispensable for Arabidopsis root microbiota. These findings not only establish a connection between root microbiota and plant epigenetic factors but also highlight the complexity of plant regulation of root microbiota.

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In silico study of the CESA and CSL gene family in Arabidopsis thaliana and Oryza sativa: Focus on post-translation modifications

Cited by 42 publications

References 81 publications

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation

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