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.
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.
Bioinformatics
Amin Abedi; Reza Shirzadian-Khorramabad; Mohamad mehdi Sohani
Volume 6, Issue 16 , March 2017, , Pages 13-29
Abstract
Strictosidine synthase is a key enzyme in the monoterpenoid indole alkaloids biosynthesis pathway. Proteins with Str_synth domain have been identified in plants, bacteria, insects and even mammalians and called Strictosidine synthase-like due to unknown functional roles. With the Arabidopsis and rice ...
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Strictosidine synthase is a key enzyme in the monoterpenoid indole alkaloids biosynthesis pathway. Proteins with Str_synth domain have been identified in plants, bacteria, insects and even mammalians and called Strictosidine synthase-like due to unknown functional roles. With the Arabidopsis and rice genome sequence completed, SSL genes were also identified in these plants. However, little is known about evolutionary path, gene structure, expansion and function of SSL family in rice. In this study, through bioinformatic analysis, a total of 23 SSL genes were identified in rice genome. A phylogenetic analysis of the SSL genes in rice and Arabidopsis clarified that these genes could be divided into four different groups and the evolutionary paths are different in rice and Arabidopsis. The OsSSL genes contained zero to five introns and were distributed across 10 out of 12 chromosomes at different densities and tandem duplication was a major cause in expanding this family. Promoter analysis showed the presence of several cis-regulatory elements related to stress and hormone response in regulatory region, indicating probable their role in stress response. Microarray-based expression analysis of OsSSL genes indicated that a few number of these genes were widely expressed in various tissues and also in response to some abiotic stresses. This study is the first report about SSL gene family in rice and provides a framework for further analysis of the biological functions of SSL genes in either rice or other crops.
Biotic and Abiotic stress
Somayeh Allahi; Mohammad Sohani; Hassan Hasani
Volume 6, Issue 15 , December 2016, , Pages 37-52
Abstract
One of the plant resistant mechanisms to abiotic stresses is production of a compatible solute named glycine betaine. Choline is the precursor of this important metabolite and it is also essential compound for the structural integrity and signaling of cell membrane. In plants, the most important step ...
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One of the plant resistant mechanisms to abiotic stresses is production of a compatible solute named glycine betaine. Choline is the precursor of this important metabolite and it is also essential compound for the structural integrity and signaling of cell membrane. In plants, the most important step of choline production is catalyzed by cytoplasmic phosphoethanolamine N-methyltransferase (PEAMT ; EC 2.1.1.103) enzyme. In this study, PEAMT gene from spinach (Spinacia oleracea Iranian landrace) was amplified using specific primers and cloned into an intermediate cloning vector (pJET). In order to overexpression of PEAMT gene, the construct of PBI121GUS-9:PEAMT was made and finally was transferred to the Agrobacterium tumefaciens GV3101 (PMP90). Floral dip method was used for transformation and initial analysis of putative transgenic plants was tested in selective medium containing kanamycin. Then resistant seedlings at the molecular level were evaluated using PCR and RT-PCR methods. Results confirmed plant transformation in the level of transcription. Subsequently, The phenotypic analysis under salt stress showed that the main root length of transgenic plants was significantly longer than control nontransgenics. In adition, glycinebetaine contents and peroxidase activity were significantly higher in transgenic compare to non-transgenics control plants.
Genetic Engineering and Gene Transformation
Amin Abedi; Mohammad Mehdi Sohani; Reza Shirzadian
Volume 5, Issue 12 , February 2016, , Pages 67-78
Abstract
The monoterpenoids comprise a family of structurally and pharmaceutically diverse alkaloids. Strictosidine synthase is a key enzyme in monoterpenoid indole alkaloid biosynthesis pathway. In spite of the apparent lack of complex alkaloids in Arabidopsis, a gene family called Strictosidine synthase like ...
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The monoterpenoids comprise a family of structurally and pharmaceutically diverse alkaloids. Strictosidine synthase is a key enzyme in monoterpenoid indole alkaloid biosynthesis pathway. In spite of the apparent lack of complex alkaloids in Arabidopsis, a gene family called Strictosidine synthase like (SSL) has been found in the genome. SSL6, a member of SSL family, has been induced significantly by various stresses and signaling molecules. An overexpressed mutant is a powerful tool for functional characterization of an unknown gene. In view of that, SSL6 overexpressed mutant have been generated in order to study the possible role of the gene in Arabidopsis defense against biotic and abiotic stresses. The open reading frame from SSL6 was amplified and cloned into intermediate pJET vector before subcloning into pPZPY122 plant vector. Plant transformation was made by floral dip method using Agrobacterium tumefaciens strain GV3101 (PMP90). The putative transgenic plants were isolated on selective MS medium containing gentamycin. Transgene integration was further analyzed by PCR using SSL6 and gentamycin resistance gene specific primers. The transcription level of SSL6 in the T2 plants was measured using q-PCR and indicated an overexpression in transgenic compared to wild type Col-0 plants. Segregation ratio of plants in T2 and T3 generation on selection medium proved that some of the genotypes contain single T-DNA insert. The SSL6 Expression level in response to salt stress was measured in Col-0 and indicated an up-regulation of the gene 3, 6 and 12 hrs after treatment.
Genetic Engineering and Gene Transformation
S Nasr-Ramzi; M Sohani; H Hasani; J Asghari
Volume 2, Issue 2 , September 2012, , Pages 49-62
Abstract
Agrobacterium-mediated transformation technique is a powerful and essential tool for genetic transformation and transgenic rice plant production. In this study an in planta transformation method was used for rice plants transformation. Therefore, rice seeds were socked for two days and the mature rice ...
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Agrobacterium-mediated transformation technique is a powerful and essential tool for genetic transformation and transgenic rice plant production. In this study an in planta transformation method was used for rice plants transformation. Therefore, rice seeds were socked for two days and the mature rice embryos was inoculated by means of an Agrobacterium coated needle. An experiment with factorial design including two strains of Agrobacterium tumefaciens (EHA105 and LBA4404) harboring pCAMBIAl105.1R, three levels of Acetosyringone (0, 100 and 200 Mµ), three cultivars of rice (Hashemi, Hasani and Gharib) and two treatments of vacuum and no vacuum operation was carried out in a Completely Randomized Design with three replications. Integration of the transgene into the genome of putative transgenic rice plants were confirmed using resistance of leaf tissues to Hygromycin, the histiochemical GUS assay and PCR with at least three different genes. Accordingly, EHA105 strain and Hashemi cultivar in the presence of 100µM acetosyringone using vacuum in a vir genes induction medium had a significant transformation efficiency (37.46%). The success of transformation was further confirmed by analysis of T1 generation with 21% transgenic.
