A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: Application to Arabidopsis

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.

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In silico analysis of promoter region and regulatory elements of glucan endo-1,3-beta-glucosidase encoding genes in Solanum tuberosum: cultivar DM 1-3 516 R44

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00240-0 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Atnafu Kebede ◽

Mulugeta Kebede

Keyword(s):

Solanum Tuberosum ◽

Disease Resistance ◽

Genetic Engineering ◽

In Silico ◽

Regulatory Elements ◽

Start Codon ◽

Predictive Score ◽

Regulation Mechanism ◽

Promoter Regions ◽

Beta Glucosidase

Abstract Background Potato (Solanum tuberosum L.) is one of the most important food crops in the world. Pathogens remain as one of the major constraints limiting potato productivity. Thus, understanding of gene regulation mechanism of pathogenesis-related genes such as glucan endo-1,3-beta-glucosidase is a foundation for genetic engineering of potato for disease resistance and reduces the use of fungicides. In the present study, 19 genes were selected and attempts were made through in silico methods to identify and characterize the promoter regions, regulatory elements, and CpG islands of glucan endo-1,3-beta-glucosidase gene in Solanum tuberosum cultivar DM 1-3 516 R44. Results The current analysis revealed that single transcription start sites (TSSs) were present in 12/19 (63.2%) of promoter regions analyzed. The predictive score at a cutoff value of 0.8 for the majority (84.2%) of the promoter regions ranged from 0.90 to 1.00. The locations for 42% of the TSSs were below −500 bp relative to the start codon (ATG). MβGII was identified as the common promoter motif for 94.4% of the genes with an E value of 3.5e−001. The CpG analysis showed low CpG density in the promoter regions of most of the genes except for gene ID102593331 and ID: 102595860. The number of SSRs per gene ranged from 2 to 9 with repeat lengths of 2 to 6 bp. Evolutionary distances ranged from 0.685 to 0.770 (mean = 0.73), demonstrating narrower genetic diversity range. Phylogeny was inferred using the UPGMA method, and gene sequences from different species were found to be clustered together. Conclusion In silico identified regulatory elements in promoter regions will contribute to our understanding of the regulatory mechanism of glucan endo-1,3-beta-glucosidase genes and provide a promising target for genetic engineering to improve disease resistance in potatoes.

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In silico analysis of promoter region and regulatory elements of mitogenome co-expressed trn gene clusters encoding for bio-pesticide in entomopathogenic fungus, Metarhizium anisopliae: strain ME1

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00191-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Getachew Bantihun ◽

Mulugeta Kebede

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Entomopathogenic Fungi ◽

Metarhizium Anisopliae ◽

In Silico ◽

Promoter Region ◽

Gene Clusters ◽

Regulatory Elements ◽

Predictive Score ◽

Promoter Regions

Abstract Background Pest control strategies almost entirely rely on chemical insecticides, which cause environmental problems such as biosphere deterioration and emergence of resistant pests. Bio-pesticide is an alternative approach, which uses organisms such as entomopathogenic fungi, Metarhizium anisopliae, to control pests. Screening such potential organism at a molecular level and understanding their gene regulation mechanism is an important approach to reduce emergence of pesticide resistance and worsening of the biosphere. Understanding promoter regions which play a pivotal role in gene regulation is crucial. In particular, identification of the promoter regions in M. anisopliae Strain ME1 remains poorly understood. To our knowledge, the mitogenome trn gene clusters of M. anisopliae Strain ME1 were not characterized. Here, we used machine learning approach to identify and characterize the promoter regions, regulatory elements, and CpG island densities of 15 protein coding genes of entomopathogenic fungi, M. anisolpliae Strain ME1. Results The current analysis revealed multiple transcription start sites (TSS) for all utilized sequences, except for promoter region genes of Pro-cob and Pro-nad5. With reference to the start codon (ATG), 85.3% of TSS was located above – 500 bp. Based on the standard predictive score at cut off value of 0.8a, the current study revealed 54.7% of predictive score greater than or equal from 0.9 promoter prediction score. Expectation maximization algorithm output identified five candidate motifs. Nonetheless, of all candidate motifs, MtrnI was revealed as the common promoter region motif with a value of 76.9% both in terms of size of binding sites and with an E value of 9.1E−054. Accordingly, we perceived that MtrnI serve as the binding site for tryptophan cluster with P value 0.0044 and C4 type zinc fingers functions as the binding site to regulate gene expression of M. anisopliae Strain ME1. The analysis revealed that mitogenome trn gene clusters of M. anisopliae Strain ME1 showed homologues evolutionary ancestor supported with a bootstrap value of 100%. Conclusion Identified common candidate motifs and binding transcription factors through in silico approach are likely expected to contribute for better understanding of gene expression and strain improvement of M. anisopliae Strain ME1 for its bio-pesticides role.

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Unusual 5'-regulatory structure and regulation of the murine Mlc1 gene: Lack of promoter-specific functional elements

Journal of Nucleic Acids Investigation ◽

10.4081/jnai.2011.2314 ◽

2011 ◽

Vol 2 (1) ◽

pp. 11

Author(s):

Darja Henseler ◽

Jonathan D. Turner ◽

Matthias Eckhardt ◽

Maaike Van der Mark ◽

Yanina Revsin ◽

...

Keyword(s):

Reporter Gene ◽

In Silico ◽

Promoter Activity ◽

Regulatory Elements ◽

Luciferase Reporter ◽

Regulatory Structure ◽

Luciferase Reporter Gene ◽

Promoter Regions ◽

Potential Promoter

The MLC1 gene is involved in an autosomal recessive neurological disorder, megalencephalic leucoencephalopathy with subcortical cysts (MLC), which is characterized by macrocephaly during the first year of life and swollen white matter (leucoencephaly). Variants of MLC1 have also been associated with psychiatric disorders such as schizophrenia, major depression and bipolar disorder. Currently, little is known about the encoded protein (MLC1). Judging from its similarity to other known proteins, it may serve as a trans-membrane transporter. However, the function of the encoded protein and its gene regulation has not been investigated successfully so far. We investigated the 5’ region of the murine Mlc1 with respect to regulatory elements for gene expression. A promoter search and an in silico analysis were conducted. Luciferase reporter gene constructs with potential promoter regions were created to study promoter activity in vitro. We found two alternative first exons for the murine Mlc1 but were not able to detect any promoter activity for the investigated reporter gene constructs in different cell lines, thus pointing to the presence of essential cis-acting elements far outside of the region. In silico analysis indicated an uncommon promoter structure for Mlc1, with CCAAT-boxes representing the only noticeable elements.

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Model and Method for Contributor’s Quality Assessment in Community Image Tagging Systems

Information and Control Systems ◽

10.31799/1684-8853-2018-4-45-51 ◽

2018 ◽

pp. 45-51

Author(s):

A. V. Ponomarev

Keyword(s):

Large Scale ◽

Wide Spectrum ◽

Preference Relation ◽

Pairwise Comparison ◽

Ground Truth ◽

Comparison Method ◽

Characteristic Matrix ◽

Image Tagging ◽

Proposed Model

Introduction: Large-scale human-computer systems involving people of various skills and motivation into the information processing process are currently used in a wide spectrum of applications. An acute problem in such systems is assessing the expected quality of each contributor; for example, in order to penalize incompetent or inaccurate ones and to promote diligent ones.Purpose: To develop a method of assessing the expected contributor’s quality in community tagging systems. This method should only use generally unreliable and incomplete information provided by contributors (with ground truth tags unknown).Results:A mathematical model is proposed for community image tagging (including the model of a contributor), along with a method of assessing the expected contributor’s quality. The method is based on comparing tag sets provided by different contributors for the same images, being a modification of pairwise comparison method with preference relation replaced by a special domination characteristic. Expected contributors’ quality is evaluated as a positive eigenvector of a pairwise domination characteristic matrix. Community tagging simulation has confirmed that the proposed method allows you to adequately estimate the expected quality of community tagging system contributors (provided that the contributors' behavior fits the proposed model).Practical relevance: The obtained results can be used in the development of systems based on coordinated efforts of community (primarily, community tagging systems).

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Faculty Opinions recommendation of Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1092082.545449 ◽

2007 ◽

Author(s):

Steven Spiker

Keyword(s):

Regulatory Elements ◽

Eukaryotic Promoter

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The Coordinated Upregulated Expression of Genes Involved in MEP, Chlorophyll, Carotenoid and Tocopherol Pathways, Mirrored the Corresponding Metabolite Contents in Rice Leaves during De-Etiolation

Plants ◽

10.3390/plants10071456 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1456

Author(s):

Xin Jin ◽

Can Baysal ◽

Margit Drapal ◽

Yanmin Sheng ◽

Xin Huang ◽

...

Keyword(s):

Higher Plants ◽

Expression Patterns ◽

Regulatory Elements ◽

Isoprenoid Biosynthesis ◽

Promoter Regions ◽

Expression Of Genes ◽

Coordinated Expression ◽

Rice Leaves ◽

Mechanistic Basis ◽

Phosphate Synthase

Light is an essential regulator of many developmental processes in higher plants. We investigated the effect of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1/2 genes (OsHDR1/2) and isopentenyl diphosphate isomerase 1/2 genes (OsIPPI1/2) on the biosynthesis of chlorophylls, carotenoids, and phytosterols in 14-day-old etiolated rice (Oyza sativa L.) leaves during de-etiolation. However, little is known about the effect of isoprenoid biosynthesis genes on the corresponding metabolites during the de-etiolation of etiolated rice leaves. The results showed that the levels of α-tocopherol were significantly increased in de-etiolated rice leaves. Similar to 1-deoxy-D-xylulose-5-phosphate synthase 3 gene (OsDXS3), both OsDXS1 and OsDXS2 genes encode functional 1-deoxy-D-xylulose-5-phosphate synthase (DXS) activities. Their expression patterns and the synthesis of chlorophyll, carotenoid, and tocopherol metabolites suggested that OsDXS1 is responsible for the biosynthesis of plastidial isoprenoids in de-etiolated rice leaves. The expression analysis of isoprenoid biosynthesis genes revealed that the coordinated expression of the MEP (2-C-methyl-D-erythritol 4-phosphate) pathway, chlorophyll, carotenoid, and tocopherol pathway genes mirrored the changes in the levels of the corresponding metabolites during de-etiolation. The underpinning mechanistic basis of coordinated light-upregulated gene expression was elucidated during the de-etiolation process, specifically the role of light-responsive cis-regulatory motifs in the promoter region of these genes. In silico promoter analysis showed that the light-responsive cis-regulatory elements presented in all the promoter regions of each light-upregulated gene, providing an important link between observed phenotype during de-etiolation and the molecular machinery controlling expression of these genes.

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Sustainable Business Model Innovations in the Value Uncaptured Manufacturing Industry: Fitting Gains—Gain Creators

Sustainability ◽

10.3390/su13105647 ◽

2021 ◽

Vol 13 (10) ◽

pp. 5647

Author(s):

Burhan ◽

Udisubakti Ciptomulyono ◽

Moses Singgih ◽

Imam Baihaqi

Keyword(s):

Business Model ◽

Environmental Quality ◽

Manufacturing Industry ◽

Design Method ◽

Pairwise Comparison ◽

Comparison Method ◽

Value Proposition ◽

Sustainable Business ◽

Sustainability Index ◽

Index Matrix

Increased manufacturing activity has an impact on environmental quality degradation. Waste generated from manufacturing activities is one of the causes. Previous studies have referred to this waste as value uncaptured. Minimizing value uncaptured is a solution to improve environmental quality. This study aims to reduce value uncaptured by converting it into value captured. This process requires a value proposition design approach because of its advantages. One of the advantages of this approach is that it can improve existing or future products/services. To do so, this research uses a case study of a furniture company. To implement a converting process, a sustainable business model is proposed to solve this problem. This business model combines several methods: value proposition design, house of value and the product sustainability index matrix. Recently, the existing value proposition problem-solving has been using the value proposition design method. This research proposed implementing a house of value to replace the fitting process. The questionnaire is developed to obtain various value uncaptured in the company. To the weight of the value uncaptured, this research utilized the pairwise comparison method. Then, the weights could represent the importance of jobs. Based on the highest weight of these jobs, the alternative gains would be selected. To provide the weight of the gain creators and value captured, the house of value method is developed. Referring to three pillars of sustainability, the value captured should be considered. This research proposed implementing a product sustainability index which in turn produces eco-friendly products. This study produces “eco-friendly products” as sustainability value captured. The sustainability business model could be an alternative policy to minimize the existence of value uncaptured.

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