In silico comparative analysis of promoters derived from plant pararetroviruses

Gupta, Dipinte; Ranjan, Rajiv

doi:10.1007/s13337-017-0410-8

Cited by 8 publications

(3 citation statements)

References 28 publications

(25 reference statements)

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“…The highest number of these elements were present in VvGLP2 and -3 promoter. In the same way, unnamed-4 is involved in the regulation of genes controlling various plant processes (Gupta and Ranjan, 2017). The element was largely found in VvGLP4 promoter.…”

Section: Common Cis-regulatory Elementsmentioning

confidence: 95%

Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Ilyas

Rahman²,

Khan³

et al. 2024

Braz. J. Biol.

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Germin-like proteins (GLPs) play an important role against various stresses. Vitis vinifera L. genome contains 7 GLPs; many of them are functionally unexplored. However, the computational analysis may provide important new insight into their function. Currently, physicochemical properties, subcellular localization, domain architectures, 3D structures, N-glycosylation & phosphorylation sites, and phylogeney of the VvGLPs were investigated using the latest computational tools. Their functions were predicted using the Search tool for the retrieval of interacting genes/proteins (STRING) and Blast2Go servers. Most of the VvGLPs were extracellular (43%) in nature but also showed periplasmic (29%), plasma membrane (14%), and mitochondrial- or chloroplast-specific (14%) expression. The functional analysis predicted unique enzymatic activities for these proteins including terpene synthase, isoprenoid synthase, lipoxygenase, phosphate permease, receptor kinase, and hydrolases generally mediated by Mn+ cation. VvGLPs showed similarity in the overall structure, shape, and position of the cupin domain. Functionally, VvGLPs control and regulate the production of secondary metabolites to cope with various stresses. Phylogenetically VvGLP1, -3, -4, -5, and VvGLP7 showed greater similarity due to duplication while VvGLP2 and VvGLP6 revealed a distant relationship. Promoter analysis revealed the presence of diverse cis-regulatory elements among which CAAT box, MYB, MYC, unnamed-4 were common to all of them. The analysis will help to utilize VvGLPs and their promoters in future food programs by developing resistant cultivars against various biotic (Erysiphe necator and in Powdery Mildew etc.) and abiotic (Salt, drought, heat, dehydration, etc.) stresses.

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Section: Common Cis-regulatory Elementsmentioning

confidence: 95%

Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Ilyas

Rahman²,

Khan³

et al. 2024

Braz. J. Biol.

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“…Sequence analysis using the Plant CARE program [22] showed that the full-length SVBV promoter contained several typical cis-acting elements, such as a TATA box, CAAT box, and potential cis-regulatory elements, including GATA motifs and TC-rich repeats. In previous research, important domains of viral promoters were generally incorporated to generate different mutants, and the driven activities were assessed in tobacco and other plants [23]. According to this prediction, a full-length SVBV promoter from the Chinese isolate (SP1) and three deletion mutants (SP2, SP3, and SP4) were constructed (Fig.…”

Section: Construction Of Expression Vectors Harboring the Full-length...mentioning

confidence: 99%

Functional analysis of a viral promoter from a strawberry vein banding virus isolate from China

Jiang

Chen

Yang

et al. 2022

Virol J

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Background Promoters are important factors affecting gene expression in cells. The driven activities of viral promoters were generally assessed to screen available promoters for transgenic and research and biotech industries. In this study, we cloned a full-length promoter from a Chinese isolate of strawberry vein banding virus (SVBV) and produced several deletion mutants for evaluation of applications in production of reporter proteins in stable transgenic plants. Methods The full-length promoter of SVBV (SP1) and its three deletion mutants (SP2, SP3, and SP4) were amplified using polymerase chain reaction. The effects of SVBV SP1, SP2, SP3, and SP4 on gene expression were evaluated using β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes. Results Transient expression assays showed that the SVBV SP1 promoter and its three deletion mutants all expressed the reporter genes, albeit at very different levels. Interestingly, transcriptional activity driven by the SP1 promoter was much higher than that of the cauliflower mosaic virus (CaMV) 35S promoter. After stable transformation of the GUS gene into Nicotiana tabacum plants, SVBV SP1-driven transgene expression was approximately 2.6-fold higher than CaMV 35S promoter-driven transgene expression. In addition, GUS gene expression levels were enhanced by co-inoculation of the plants with the SP1 promoter-driven vector carrying the GUS gene and the vector expressing SVBV open reading frame (ORF) V or ORF VI. Conclusions The SVBV SP1 promoter from the Chinese isolate evaluated in this study could successfully drive transient and stable expression in plants, it was a stronger promoter than the CaMV 35S and FLt-US promoters and may be more useful for the production of stable transgenic plants.

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“…The common promoter motif is the key signature for a family of co-regulated genes and is usually present in the regions where complex protein interactions occur [ 30 ]. It is also reported that genes having similar expression patterns contain common motifs in their promoter regions [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072

Senbeta

Kebede

2021

Journal of Genetic Engineering and Biotechnology

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Background In silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the genomes. Therefore, a computational survey was carried out for the Trametes hirsuta strain 072 genome with the open reading frames from the National Center for Biotechnology Information database. Seventeen functional sequences were used to analyze promoter regions and their regulatory elements. Result The present study revealed that 94% of Trametes hirsuta strain 072 genes contained more than two TSSs. Among these identified TSSs, a TSS with the highest predictive score was considered to determine a promoter region of the genes. Moreover, a total of five common candidate motifs such as MotI, MotII, MotIII, MotIV, and MotV were identified. Among these motifs, motif IV was investigated as the common promoter motif for 41.17% of genes that serve as binding sites for transcription factors (TFs) involved in the expression regulation of Trametes hirsuta strain 072 genes. Motif IV was also compared to registered motifs in publically available databases to see if they are similar to known regulatory motifs for TF using TOMTOM web server. Hence, it was revealed that MotIV might serve as the binding site mainly for the leucine zipper TF gene family to regulate a gene expression of Trametes hirsuta strain 072. Regarding CpG island determination, it was concluded that there is no CpG island in both promoter and gene body regions of the Trametes hirsuta strain 072 genome. Conclusions This study provides a better insight into further molecular characterization which aimed to efficiently exploit a white rot fungus, Trametes hirsuta strain 072, for several biotechnological applications aimed to revitalize a severely contaminated environment.

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In silico comparative analysis of promoters derived from plant pararetroviruses

Cited by 8 publications

References 28 publications

Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Functional analysis of a viral promoter from a strawberry vein banding virus isolate from China

Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072

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