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.
Bioinformatics
Seyyed Mohsen Sohrabi; Ali Akbarabadi; Kamran Samiei; Anahita Panji
Abstract
Tomato (Solanum lycopersicum) is an annual, self-pollinated and diploid plant belonging to the potato family (Solanaceae). Different types of this plant form an important part of the world's diet. Bacterial diseases are one of the most important factors limiting tomato production worldwide. In the present ...
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Tomato (Solanum lycopersicum) is an annual, self-pollinated and diploid plant belonging to the potato family (Solanaceae). Different types of this plant form an important part of the world's diet. Bacterial diseases are one of the most important factors limiting tomato production worldwide. In the present study, by using transcriptome (RNA-seq) analysis followed by gene network analysis, the key genes involved in response to bacterial diseases were identified and their various characteristics were investigated. The results of the transcriptome analysis showed that bacterial pathogens have different effects on the transcriptome of tomato. Further analysis revealed 913 common differentially expressed genes among different bacterial treatments. Network analysis identified five key genes named large guanine nucleotide binding protein, mitogen-activated protein kinase 5, mitogen-activated protein kinase 7, heat shock protein 90 kDa and hop-interacting protein. Further analysis of identified key genes showed that all of them contain biotic stress related regulatory elements (w-box, WRE3 and WUN-motif) in their promoter region and have an important role in responding to biotic stresses. The key genes identified in this research can be used in classic breeding programs or in production of disease-resistant transgenic plants after a more detailed examination.
Keywords: Gene networks, Plant breeding, Plant diseases, Tomato, Transcriptome
Bioinformatics
Hadis Boroun; Amir Siahpoosh; Seyyed Mohsen Sohrabi; Mohammad Reza Nikbakht; Javad Ghasemian Yadegari; Mohsen Mohammadi; Seyed Sajad Sohrabi
Abstract
Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin ...
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Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin gene family members were identified and characterized from onion (Allium cepa L.) using bioinformatics and experimental methods. All snakin protein sequences were retrieved from NCBI database. The snakin consensus sequence was obtained from alignment of retrieved sequences. Then, the consensus sequence was aligned against the onion transcriptome using tBLASTn tool. The resulting sequences were analyzed to determine the full-ORF, and to prediction of functional domains, signal peptides, subcellular localization, physicochemical properties, amino acid frequency and anti-microbial activity. The complete coding sequence of snakin genes were amplified by PCR. Finally, the presence of seven snakin genes, with an average ORF length of 332 bp, were confirmed in onion. The high similarity of the onion snakin genes with homologous snakin genes belonging to other plant species in terms of nucleotide and protein sequences as well as structural was revealed by bioinformatics analysis. The results also showed that all identified onion snakins had the potential antimicrobial activity. Due to the potential antimicrobial activity of identified peptides, by producing these peptides in different expression systems, they can be used as new antimicrobial agents against human, animal and plant pathogens.