scholarly journals In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184523 ◽  
Author(s):  
Amritpreet Kaur ◽  
Pratap Kumar Pati ◽  
Aparna Maitra Pati ◽  
Avinash Kaur Nagpal
Keyword(s):  
Arabidopsis Thaliana ◽  
Oryza Sativa ◽  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Pathogenesis Related Proteins ◽  
Cis Acting ◽  
Pathogenesis Related ◽  
Related Proteins ◽  
Silico Analysis

scholarly journals Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10053
Author(s):  
Fernando Carlos Gómez-Merino ◽  
Libia Iris Trejo-Téllez ◽  
Atonaltzin García-Jiménez ◽  
Hugo Fernando Escobar-Sepúlveda ◽  
Sara Monzerrat Ramírez-Olvera
Keyword(s):  
Plant Growth ◽  
Plant Species ◽  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Plant Tissues ◽  
Promoter Regions ◽  
Root Cells ◽  
Physiological Processes ◽  
Silico Analysis

Background Silicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data. Methods We established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L−1 Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis. Results Si concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors. Conclusion Pepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper.

scholarly journals FRUITFULL Is a Repressor of Apical Hook Opening in Arabidopsis thaliana

2020 ◽  
Vol 21 (17) ◽  
pp. 6438
Author(s):  
Miriam Führer ◽  
Angelika Gaidora ◽  
Peter Venhuizen ◽  
Jedrzej Dobrogojski ◽  
Chloé Béziat ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
In Silico ◽  
Target Genes ◽  
Growth Promotion ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Suitable Model ◽  
Differential Growth ◽  
Apical Hook ◽  
Growth Transitions

Plants adjust their architecture to a constantly changing environment, requiring adaptation of differential growth. Despite their importance, molecular switches, which define growth transitions, are largely unknown. Apical hook development in dark grown Arabidopsis thaliana (A. thaliana) seedlings serves as a suitable model for differential growth transition in plants. Here, we show that the phytohormone auxin counteracts the light-induced growth transition during apical hook opening. We, subsequently, identified genes which are inversely regulated by light and auxin. We used in silico analysis of the regulatory elements in this set of genes and subsequently used natural variation in gene expression to uncover correlations between underlying transcription factors and the in silico predicted target genes. This approach uncovered that MADS box transcription factor AGAMOUS-LIKE 8 (AGL8)/FRUITFULL (FUL) modulates apical hook opening. Our data shows that transient FUL expression represses the expression of growth stimulating genes during early phases of apical hook development and therewith guards the transition to growth promotion for apical hook opening. Here, we propose a role for FUL in setting tissue identity, thereby regulating differential growth during apical hook development.

scholarly journals In Silico Analysis of Pacific Oyster (Crassostrea gigas) Transcriptome over Developmental Stages Reveals Candidate Genes for Larval Settlement

2019 ◽  
Vol 20 (1) ◽  
pp. 197 ◽  
Author(s):  
Valentin Foulon ◽  
Pierre Boudry ◽  
Sébastien Artigaud ◽  
Fabienne Guérard ◽  
Claire Hellio
Keyword(s):  
Crassostrea Gigas ◽  
In Silico ◽  
Pacific Oyster ◽  
Developmental Stages ◽  
Larval Settlement ◽  
In Silico Analysis ◽  
Suitable Habitat ◽  
Related Proteins ◽  
Von Willebrand ◽  
Silico Analysis

Following their planktonic phase, the larvae of benthic marine organisms must locate a suitable habitat to settle and metamorphose. For oysters, larval adhesion occurs at the pediveliger stage with the secretion of a proteinaceous bioadhesive produced by the foot, a specialized and ephemeral organ. Oyster bioadhesive is highly resistant to proteomic extraction and is only produced in very low quantities, which explains why it has been very little examined in larvae to date. In silico analysis of nucleic acid databases could help to identify genes of interest implicated in settlement. In this work, the publicly available transcriptome of Pacific oyster Crassostrea gigas over its developmental stages was mined to select genes highly expressed at the pediveliger stage. Our analysis revealed 59 sequences potentially implicated in adhesion of C. gigas larvae. Some related proteins contain conserved domains already described in other bioadhesives. We propose a hypothetic composition of C. gigas bioadhesive in which the protein constituent is probably composed of collagen and the von Willebrand Factor domain could play a role in adhesive cohesion. Genes coding for enzymes implicated in DOPA chemistry were also detected, indicating that this modification is also potentially present in the adhesive of pediveliger larvae.

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