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.
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.
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.
Bioinformatics
Zahra Pakbaz; Asa Ebrahimi; Martina Rickauer; Cecile Ben; Abdollah Mohammadi
Abstract
Metal tolerance proteins (MTP) are plant membrane divalent cation transporters, which plays an important role during plant growth and development. They involve in minerals uptake and provide resistance for plants in polluted soil by heavy metal. However, information about MTPs proteins in Fabceace family ...
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Metal tolerance proteins (MTP) are plant membrane divalent cation transporters, which plays an important role during plant growth and development. They involve in minerals uptake and provide resistance for plants in polluted soil by heavy metal. However, information about MTPs proteins in Fabceace family are scarcely known. Therefore, in this study we provided an extensive evaluation of MTP genes in three important members of this family including: Glycine max, Medicago truncatula and Phaseolus vulgaris by providing phylogenetic assessments, chromosomal distributions, gene structures and expression in different tissue. According to the results 14, 12 and 23 MTP genes respectively were found in M. truncatula, P. vulgaris and G. max. 13 duplicated MTP genes in G. max were found meanwhile we did not find any duplication in the MTP genes of M. truncatula and P. vulgaris. All studied MTPs were classified into three major cation diffusion facilitator (CDFs) groups; Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. In silico subcellular location results revealed that these proteins have the maximum activity in the vacuole in all three plants, and a small number are located in the cell wall and nucleus. According to gene structure and protein motifs of studied MTPs, they are highly conserved but their expression measurement showed that each one of them have different levels of expression during growth stage. It confirms their importance for plants during growth and development.
Bioinformatics
Naser Mohammadian Roshan
Abstract
Growth regulating factors (Growth Regulatory Factors) are plant-specific transcription factors which contain two conserved domains, QLQ and WRC. Members of this family are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. In this ...
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Growth regulating factors (Growth Regulatory Factors) are plant-specific transcription factors which contain two conserved domains, QLQ and WRC. Members of this family are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. In this study, wheat GRF genes were identified and analysis by bioinformatics methods. GRF genes identification was performed by blastP. Then evolutionary relationships, gene structure, promoter, miRNA, gene ontology and expression of identified genes were analyzed. 30 TaGRFs (TaGRF1–30) distributed on 12 chromosomes were identified by searching wheat genome database and were clustered into six subgroups according to their phylogenetic relationships. TaGRFs belonging to the same subgroup shared a similar motif composition and gene structure. They all contain two conserved motifs (QLQ and WRC) and have 2–5 exons. Due to the identification of stresses, hormones and tissue specific cis elements in the TaGRFs promoter, these genes are involved in many biological processes of wheat. MiR396 target analysis indicated that 26 GRFs mRNA contained miRNA396 target position in wheat. RNA-seq data from the expVip database showed that TaGRF1, TaGRF4 and TaGRF7 were strongly expressed in root, shoot, leave, spike and grain in vegetative and reproductive stages. This data also indicated that all TaGRF genes except TaGRF16 were expressed in vegetative stage of spike. The results of this study provide the evolutionary and functional information needed for Design of functional studies of this gene family.
Bioinformatics
Alireza Ladan Moghdam
Abstract
Brassinosteroids (BRs) are the plant-specific steroidal hormones that regulate a broad spectrum of plant growth and developmental processes under normal conditions and various biotic, and abiotic stresses. BES1 transcription factors regulate the expression of brassinosteroid-responsive genes. Completion ...
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Brassinosteroids (BRs) are the plant-specific steroidal hormones that regulate a broad spectrum of plant growth and developmental processes under normal conditions and various biotic, and abiotic stresses. BES1 transcription factors regulate the expression of brassinosteroid-responsive genes. Completion of the grape genome sequencing enabled us to undertake a genome-wide identification of the gene families in this plant. Therefore, we performed a genome-wide investigation of BES genes in grape. The physicochemical properties, phylogeny tree, gene structure, conserved motifs, cis-acting elements, miRNA, and gene chip expression of the grape BES1 transcription factors were analyzed using the bioinformatics tools. The results showed that the grape BES1 transcription factors had seven members, which clustered into three subgroups according to the phylogenetic analysis. Each subgroup was well defined by the conserved motifs, implying that close genetic relationships could be identified among the members of each subgroup. According to the chromosomal locations, 1, 1, 2, 1, 1, and 1 genes were located on chromosomes 2, 4, 10, 15, 18, and 19, respectively. The analysis of cis-acting elements indicated that BES1 genes contained response elements of hormones and abiotic stresses, as well as organ-specific elements. The miRNA target analysis indicated that VvBES1-1, VvBES1-3, and VvBES1-5 contained miRNA target position in grape. Gene chip expression profile analysis revealed that the expression patterns of the grape BES1 genes were different in different organs and developmental stages. The analysis of this gene family would provide some theoretical basis for understanding the evolution and function of the BES1 genes in the grape.
Bioinformatics
Behnaz Karami Lake; Mohammad Sohani; Amin Abedi
Abstract
The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. In the present study, using related database, 14 CaCA genes were identified in the maize genome and classified according to their structural ...
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The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. In the present study, using related database, 14 CaCA genes were identified in the maize genome and classified according to their structural organization and evolutionary association with the identified CAX, CCX and MHX proteins. Most of the ZmCaCA proteins had two Na_Ca_ex domains. All of the identified genes had at least one functional motif and gene structure of each CaCA subgroup is highly conserved. In the prediction of reactive miRNAs relative to CaCA genes in maize, 33 different miRNA variants were identified that regulate the expression of 13 CaCA genes through cleavage or inhibition of translation. In addition, several cis-acting regulatory elements in ZmCaCA genes were found to be related to hormones stress responses. The variable expression of most ZmCaCA genes at different stages of development indicates their distinct role in development. Expression of these genes in abiotic stresses (cold, salt, and drought) indicates their role in stress response. The greatest high expression and down regulation of gene expression is related to CAX genes. The results of this study provide basic data about phylogeny and putative function of these genes for future studies on the role of CaCA genes in maize.
Molecular Plant Breeding
Sajjad Zare; Farhad Nazarian-Firouzabadi; Ahmad Ismaili; Hassan Pakniyat
Abstract
Study of stress tolerance in barley can help for a better understanding of the genetic basis of drought stress tolerance mechanisms and lead to improve the genetic properties associated with drought tolerance through modern molecular genetic techniques. To this end, microRNAs associated with drought ...
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Study of stress tolerance in barley can help for a better understanding of the genetic basis of drought stress tolerance mechanisms and lead to improve the genetic properties associated with drought tolerance through modern molecular genetic techniques. To this end, microRNAs associated with drought stress in barley leaf and root ESTs were analyzed in Nimruz and spantaneum barley genotypes. Bioinformatics databases were mined for relevant EST libraries and bioinformatics services were used for pre-processing and identify genes with different expressions among libraries. The expression profile of candidate genes was studied, by using Real time-PCR in a factorial-split plot design, including Nimruz as tolerant and Spontaneum as a drought sensitive in pots with three replications. Sampling time was also considered at 0, 24 and 72 hours after drought stress as sub factor. Results of this study led to identification of three highly-expressed miRNAs (ath-miR414, os-miR2102-5p and osa-miR414). The expression analysis showed that miR414 and miR2102 expression was significantly (P< 0.05) increased in both genotypes in response to drought stress. After 72h in Nimruz and Spontaneum, the expression of miR414 reached 2.61 and 2-fold and the expression of miR2102 was 2.4 and 2.8-fold of that of control (Spontaneum at control condition at 0 times), respectively.
Bioinformatics
Amin Abedi; Reza Shirzadian-Khorramabad; Mohammad Mehdi Sohani
Volume 7, Issue 18 , November 2017, , Pages 27-40
Abstract
In eukaryotes cells, genomic DNA in combination with histone proteins is formed the chromatin. Histone chaperones affect the gene transcription via altering in DNA accessibility. In contrast to their animal and yeast counterparts, not much is known about plant histone chaperones. Nucleosome assembly ...
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In eukaryotes cells, genomic DNA in combination with histone proteins is formed the chromatin. Histone chaperones affect the gene transcription via altering in DNA accessibility. In contrast to their animal and yeast counterparts, not much is known about plant histone chaperones. Nucleosome assembly protein (NAP) family histone chaperones are conserved throughout eukaryotic genomics. NAP is an integral component in the establishment, maintenance, and dynamics of eukaryotic chromatin. They transfer histones into the nucleus, assemble nucleosomes, and promote chromatin fluidity, thereby, affecting the transcription of many genes. In this study, by applying some bioinformatics analysis approaches, six putative NAP genes (ZmNAPL1–ZmNAPL6) were identified in maize (Zea mays) using the released maize genomic sequences. Phylogenetic analysis showed that these ZmNAPLs are classified into two subgroups as found in Arabidopsis and rice. Moreover, it was found that maize NAPL proteins are more closely related to rice. The ZmNAPL genes contained three to eleven introns and were distributed across 5 out of 20 chromosomes in maize. Microarray-based expression analysis of ZmNAPLs showed that there is a tight transcriptional regulation on ZmNAPL genes during the plant development in maize suggesting that they may play a role in genetic reprogramming in association with the developmental process. This study is the first report about NAPL gene family in maize and obtained results provide basic information for future research on the functions of NAPL genes in maize.
