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 ...
Read More
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.
Bioinformatics
Samira Mohammadi; Ghorbanali Nematzadeh; Hamid Najafi Zarini; Seyyed Hamidreza Hashemi-petroudi
Abstract
MicroRNAs are a large class of small and non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. Plant miR164 family is highly conserved and is involved in the responses of plants to biotic stresses through the regulation of their target ...
Read More
MicroRNAs are a large class of small and non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. Plant miR164 family is highly conserved and is involved in the responses of plants to biotic stresses through the regulation of their target NAC genes. In the present study, 68 putative NAC domain-encoding genes (NACs) were identified in Aeluropus littoralis, a halophyte plant of family Poaceae. Among the AlNAC genes identified, 4 were predicted putative targets for regulation by miR164. The high conservation of miR164 recognition sites in AlNAC genes indicates the essential role of target sites in the normal function of these genes as transcription factors. Expression profile of AlNAC1L.1 candidate gene in response to salt and drought stresses and ABA phytohormone in leaf, stem and root tissues was analyzed by RT-qPCR. The results showed that AlNAC1L.1 gene down-regulated in all tissues at 6 hours after applying stresses. Among the treatments, 600 mM NaCl treatment reduced AlNAC1L.1 expression in leaf, stem and root tissues to about -217, -26 and -9 folds, respectively. Therefore, the AlNAC1L.1 which is ortholog of known Oryza miR164-targeted NAC gene OMTN6, may play negative regulatory role in response to salt, drought and ABA treatments. These results indicated that function of some NAC proteins might be conserved among species. Collectively, these findings provided a useful resource for further analysis of the interactions between NAC genes and their intricate regulation by miR164 in response to abiotic stresses.
Molecular Plant Breeding
Sahar Faraji; Seyyed Hamidreza Hashemi-Petroudi; Hamid Najafi-Zarrini; Gholamali Ranjbar
Volume 7, Issue 20 , March 2018, , Pages 13-27
Abstract
Salinity is considered as a perilous environmental stress reducing crop yields, which makes the plant survive difficult via stopping the various mechanisms of it, eventually leading to death. Genes are the momentous factors in multiple physiological pathways regarding to their involvements in stress ...
Read More
Salinity is considered as a perilous environmental stress reducing crop yields, which makes the plant survive difficult via stopping the various mechanisms of it, eventually leading to death. Genes are the momentous factors in multiple physiological pathways regarding to their involvements in stress responses. The gene encoding for Chromodomain Helicase DNA protein (PICKLE, PKL) is one of them, which regulates the other stress-responsive genes transcriptions under unfavorable conditions. Transcripts assay in halophyte Aeluropus littoralis, as a valuable genetic resource, will provide the inspiring information for sensitive crops improvement. Therefore, biochemical properties, functional domains, phylogenetic analysis and promoter cis-elements were investigated in this study, suggesting that this gene may play the critical roles in dealing with stimulus circumstances. Expression profiling of AlPKL in coping with salinity and recovery situations in A. littoralis shoot and root tissues through the qReal-Time PCR technique was also revealed high transcript magnitudes of this gene. Hence, further studies on PKL genes in multiple plant species can provide precious information for better understanding of stress endurance mechanisms.
Proteomics
Maryam Jamshidnia; Sayed Kamal Kazemitabar; Christian Lindermayr; Hamid Najafi Zarini
Volume 6, Issue 16 , March 2017, , Pages 1-12
Abstract
Recently, transient gene expression has been developed to provide a more rapid means of assessing plant tissues as a protein production platform without the labor-intensive and time-consuming process of generating stably transformed transgenic plants. This study reports the expression of HDA19 gene in ...
Read More
Recently, transient gene expression has been developed to provide a more rapid means of assessing plant tissues as a protein production platform without the labor-intensive and time-consuming process of generating stably transformed transgenic plants. This study reports the expression of HDA19 gene in two species of tobacco plants (Nicotiana tabacum and Nicotiana bentamiana) by means of transient transformation. Specific primers were designed and used for PCR amplification and cloning of HDA19 gene in the plant expression vector pB2GW7. The recombinant construct was transferred into Agrobacterium tumefaciens strain GV3101, and was used for Agrobacterium mediated transformation of tobacco plants. The presence of the desired gene in transgenic lines was confirmed through colony PCR. The expression of the protein in transgenic lines was confirmed by immune-dot blot assay and ELISA. Although the transformation of the two species was confirmed by immune-dot blot assay and SDS-PAGE, recombinant protein production in Nicotiana tabacum plants was confirmed by ELISA and it was estimated 400 µg per gram wet weight of tobacco leaves. According to the results, this species is the appropriate host for the production of recombinant HDA19, one of the histone deacetylases, rather than Nicotiana bentamiana.
