Research Paper
Bioinformatics
Anahita Panji; Ahmad Ismaili; Seyyed Mohsen Sohrabi
Abstract
Antimicrobial peptides are a part of the innate immune system in plants. They are present in all tissues and a wide range of plant species, and their antimicrobial effect against plant and animal pathogens and cancer cells has been proven. Snakins are a group of low molecular weight cysteine-rich plant ...
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Antimicrobial peptides are a part of the innate immune system in plants. They are present in all tissues and a wide range of plant species, and their antimicrobial effect against plant and animal pathogens and cancer cells has been proven. Snakins are a group of low molecular weight cysteine-rich plant antimicrobial peptides involved in the defense against biotic and abiotic stresses, hormone pathways, and plant growth and development. In the present study, laboratory and bioinformatic methods were used to investigate the characteristics of the snakin gene family members and to evaluate their expression changes in four seed development stages (3, 8, 13, and 18 days after pollination) in barley plants. The results showed the presence of 11 snakin genes in the genome of barley. The protein sequences of the identified snakins contained the GASA functional domain. These snakins had a signal peptide and had extracellular accumulation. Due to their high abundance of hydrophobic amino acids, they were hydrophobic and produced complex secondary structures. Phylogenetic analysis was performed between barley, rice, and arabidopsis snakins as two monocot and dicot models, leading to three classes. Also, six disulfide bonds and antimicrobial properties were computationally confirmed in all identified proteins. Expression analysis showed different expression patterns for snakin gene family members in different stages of seed development and also exhibited different trends in each stage. The snakin genes can use to produce transgenic plants and to produce a new generation of natural antibiotic agents to protect humans, plants, and animals.
Research Paper
Bioinformatics
Mohammad Mohsenzadeh Golfazani; Alireza Tarang; Ramin Seighalani
Abstract
There is much information about the regulation of gene expression in response to various stresses at the transcriptional level. Nevertheless, there is limited information about this process at the post-transcriptional level. The diversity and complexity of miRNA regulation indicates their importance ...
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There is much information about the regulation of gene expression in response to various stresses at the transcriptional level. Nevertheless, there is limited information about this process at the post-transcriptional level. The diversity and complexity of miRNA regulation indicates their importance in biological processes. Many miRNA regulatory modules can form a complex miRNA-mRNA regulatory network. Therefore, research on miRNA-mRNA regulatory networks can provide valuable information for understanding complex biological processes. These data are very important to further study the stress tolerance mechanisms in plants, especially in rapeseed. In this research, the selection of miRNAs related to drought and salinity stress was made by reviewing the articles on abiotic stresses. Then the target genes were identified using the sequences of mature miRNAs and psRNATarget online software. A gene list of 225 identified target genes was prepared using the UniProt database. Their functional pathway was identified utilizing the DAVID bioinformatics database and KEGG database according to default parameters. Investigations showed that these target genes were involved in several biological pathways including ribosome, spliceosome, proteasome, purine metabolism, selenocompound metabolism, and sulfur metabolism. In addition, the STRING database was used to check co-expression genes. Our result indicated the existence of 37 co-expression genes among the identified target genes.
Research Paper
Bioinformatics
Seyyed Hamidreza Hashemi-petroudi; Samira Mohammadi; Esmaeil Bakhshandeh; Markus Kuhlmann
Abstract
From prokaryotes to higher eukaryotes, protein phosphatase 2Cs (PP2Cs) play a critical role in the stress response. For the purpose of identifying the AlPP2C gene and examining its expression, Aeluropus littoralis, a salt-secreting halophytic grass belonging to the Poaceae family, was genome-wildly analyzed. ...
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From prokaryotes to higher eukaryotes, protein phosphatase 2Cs (PP2Cs) play a critical role in the stress response. For the purpose of identifying the AlPP2C gene and examining its expression, Aeluropus littoralis, a salt-secreting halophytic grass belonging to the Poaceae family, was genome-wildly analyzed. Based on the unique structure of the PP2C domain, 34 AlPP2C genes were discovered and classified into ten evolutionary branches based on homology with Arabidopsis thaliana. According to exon-intron structural analyses, they possessed a wide range of exon counts. AlPP2Cs shared similar motif organization in the same evolutionary branches based on motif distribution. The motifs ABRE, MBS, DRE, STRE, and LTR, which are related with stress, were discovered in the promoter region of the AlPP2C. AlPP2Cs displayed varied expression patterns in leaf and root tissues in response to salt stress and recovery conditions, according to transcriptome analyses. The AlPP2C4 gene is only expressed in the root tissues. These results expand our understanding of the PP2C gene family and provide valuable information for future research on PP2Cs molecular function and biological processes studies.
Research Paper
Bioinformatics
Mahin Pouresmaeil; Maghsoud Pazhouhandeh
Abstract
Today, the genome sequence of most organisms has been identified, and this information is useful in understanding the function and characteristics of organisms. In the meantime, there is unprocessed information that can be used to study unknown proteins and genes with the advancement of technology and ...
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Today, the genome sequence of most organisms has been identified, and this information is useful in understanding the function and characteristics of organisms. In the meantime, there is unprocessed information that can be used to study unknown proteins and genes with the advancement of technology and the use of bioinformatics tools. In this research, the sequence of a gene with unknown function from Arabidopsis thaliana with accession number of X91953.1 in NCBI database was used to investigate and study its structure and possible function. This gene is related to chromosome number one in Arabidopsis thaliana and with 676 base pairs, it produces a protein with 150 amino acids and a molecular weight of approximately 15 kD. By using bioinformatics servers, the characteristics of both gene and protein sequences were investigated and it was found that it has 18 types of regulatory motifs, the functions of some of which are known, which can be related to the response to light and the activity of Cis elements for expression in the meristem. The analyzes showed that this protein has 38 motifs, three of them are conserved with high frequency. This protein has a signal peptide at its Nt and is leaked into the extracellular space. Therefore, its presence in the intercellular space is more likely than the nucleus and intracellular organelles. There is also a regulation site of a microRNA on its transcript and this microRNA is active in response to salinity and also in the embryo. This unknown protein has about 90% homology with another protein in Arabidopsis with accession number of UPF0540 (At1g62000), which can be used for further studies to identify the role of the desired protein. This protein is expressed in 10 different tissues, mainly in embryo and seed endosperm. Based on all the analyzes carried out, two functions of seed coat differentiation and the biosynthesis of secreted substances due to light can be predicted for this protein. In the continuation of this work, laboratory methods are recommended for testing the functions attributed to this gene.
Research Paper
Genetic Engineering and Gene Transformation
Mohamad Amin Neycee; Motahhareh Mohsenpour; Hassan Rahnama
Abstract
Safflower with low oleic acid content is one of the native plants of Iran. Generally,, high oleic acid oils have more oxidative stability than the oils with high linoleic acids . Genome editing technology enable us to obtain oilseeds with high oleic acid. In this research, two guide RNA sequences ...
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Safflower with low oleic acid content is one of the native plants of Iran. Generally,, high oleic acid oils have more oxidative stability than the oils with high linoleic acids . Genome editing technology enable us to obtain oilseeds with high oleic acid. In this research, two guide RNA sequences were designed to target of Fatty Acid Desaturase 2 (FAD2-1) gene, which were located within the coding region and at a distance of 640 base pairs from each other. The guide sequences along with the codon optimized Cas9 gene were cloned in the T-DNA region of the Agrobacterium construct and transferred to the safflower by the In-planta method. The resulting seeds were cultivated and the plants were screened to track changes in the fatty acid profile of the seeds. The results showed that the amount of oleic acid in the seeds of one of the lines reached 53.14% on average. This line had four amino acid changes (L66F, N204D, S236A and I238V) at the same time. This is while the amount of oleic acid in the control plant was measured as 11.62% on average. The results showed that in the segregating generation, the change in fatty acid profile occurred in the line with homozygous amino acid change, and the heterozygous plants have the same oil profile as the control plants. Also, the results of this research can indicate the possibility of increasing the amount of oleic acid in oilseeds by changing the FAD2 enzyme sequence and without gene knockout.
Research Paper
Bioinformatics
Parisa Ramezanpoor; Hamid Najafi Zarini; Hamidreza Hashemi; Gholamali Ranjbar
Abstract
Zincfinger CCCH (C3HZNF) genes encode proteins with three cysteines and one histidine. The proteins of this family are an important group of zinc finger transcription factors that are effective in various activities such as plant growth and response to biotic and abiotic stresses and actually They are ...
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Zincfinger CCCH (C3HZNF) genes encode proteins with three cysteines and one histidine. The proteins of this family are an important group of zinc finger transcription factors that are effective in various activities such as plant growth and response to biotic and abiotic stresses and actually They are effective in stresses tolarance. In this article, C3HZNF protein data of Arabidopsis and rice plants were used to analyze phylogenetic relationships, exon/intron structure, motifs/domains organization. These studies showed the high homology of these genes with CCCH genes in rice. Analysis of the gene structure showed that AtC3Hs have a variable number of exons, but in general, genes with 1 and 7 exons contain the largest number. study the physical and chemical properties of this family showed that AtC3H36 is the most stable protein among the members of this family, and the highest isoelectric point belongs to the AtC3H7(9.96) protein. The observations showed that the members of this gene family have 1 to 6 Znf C3H domains and a total of 17 functional domains. Phylogeny comparison between C3H proteins in rice and Arabidopsis showed that these proteins are highly conserved. In the comparative phylogenetic analysis of AtC3H and OsC3H, the orthologous genes were placed in one group. For example, OsC3H8 showed close homology to HUA1 in Arabidopsis (AtC3H37), suggesting that this gene is involved in flower development. This study provides valuable information about the important CCCH zinc finger gene family in Arabidopsis and rice. This information can be helpful in understanding how these genes work to help plant tolarance when faced with biotic and abiotic stresses.
