scholarly journals Identification, expression analysis and molecular modeling of Iron deficiency specific clone 3 (Ids3) like gene in hexaploid wheat

2018 ◽  
Author(s):  
Priyanka Mathpal ◽  
Upendra Kumar ◽  
Anuj Kumar ◽  
Sanjay Kumar ◽  
Sachin Malik ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Expression Analysis ◽  
Physical Mapping ◽  
Hexaploid Wheat ◽  
Bioinformatics Analysis ◽  
Wheat Cultivar ◽  
Wheat Chromosome ◽  
Telomeric Region ◽  
Iron Starvation ◽  
Mugineic Acid Family Phytosiderophores

AbstractGraminaceous plants secrete iron (Fe) chelators called mugineic acid family phytosiderophores (MAs) from their roots for solubilisation and mobilization of unavailable ferric (Fe3+) ions from the soil. The hydroxylated forms of these phytosiderophores have been found more efficient in chelation and subsequent uptake of minerals from soil which are available in very small quantities. The genes responsible for hydroxylation of phytosiderophores have been recognized as iron deficiency-specific clone 2 (Ids2) and iron deficiency-specific clone 3 (Ids3) in barley but their presence is not reported earlier in hexaploid wheat. Hence, the present investigation was done with the aim:(i) to search for the putative Hordeum vulgare Ids3 (HvIds3) ortholog in hexaploid wheat, (ii) physical mapping of HvIds3 ortholog on wheat chromosome using cytogenetic stocks developed in the background of wheat cultivar Chinese Spring and (iii) to analyze the effect of iron starvation on the expression pattern of this ortholog at transcription level. In the present investigation, a putative ortholog of HvIds3 gene was identified in hexaploid wheat using different bioinformatics tools. Further, protein structure of TaIDS3 was modelled using homology modeling and also evaluated modelled structure behavior on nanoseconds using molecular dynamics based approach. Additionally, the ProFunc results also predict the functional similarity between the proteins of HvIds3 and its wheat ortholog (TaIds3). The physical mapping study with the use of cytogenetic stocks confines TaIds3 in the telomeric region of chromosome 7AS which supports the results obtained by bioinformatics analysis. The relative expression analysis of TaIds3 indicated that the detectable expression of TaIds3 induces after 5th day of Fe-starvation and increases gradually up to 15th day and thereafter decreases till 35th day of Fe-starvation. This reflects that Fe deficiency directly regulates the induction of TaIds3 in the roots of hexaploid wheat.

scholarly journals Identification, expression analysis, and molecular modeling of Iron-deficiency-specific clone 3 (Ids3)-like gene in hexaploid wheat

3 Biotech ◽  
2018 ◽  
Vol 8 (4) ◽  
Author(s):  
Priyanka Mathpal ◽  
Upendra Kumar ◽  
Anuj Kumar ◽  
Sanjay Kumar ◽  
Sachin Malik ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Iron Deficiency ◽  
Expression Analysis ◽  
Hexaploid Wheat

Molecular Cloning, Physical Mapping, and Expression Analysis of a Novel Gene, BCL2L12, Encoding a Proline-Rich Protein with a Highly Conserved BH2 Domain of the Bcl-2 Family

Genomics ◽  
2001 ◽  
Vol 72 (2) ◽  
pp. 217-221 ◽  
Author(s):  
Andreas Scorilas ◽  
Lianna Kyriakopoulou ◽  
George M. Yousef ◽  
Linda K. Ashworth ◽  
Aku Kwamie ◽  
...  
Keyword(s):  
Molecular Cloning ◽  
Expression Analysis ◽  
Physical Mapping ◽  
Novel Gene ◽  
Proline Rich Protein

scholarly journals Genome-Wide Identification and Expression Analysis of GA2ox, GA3ox, and GA20ox Are Related to Gibberellin Oxidase Genes in Grape (Vitis Vinifera L.)

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 680 ◽  
Author(s):  
He ◽  
Liang ◽  
Lu ◽  
Wang ◽  
Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Real Time ◽  
Expression Analysis ◽  
Bioinformatics Analysis ◽  
Expression Profiles ◽  
Biologically Active ◽  
Vitis Vinifera L ◽  
Genome Database ◽  
Qrt Pcr ◽  
Grape Genome

Gibberellin (GAs) plays the important role in the regulation of grape developmental and growth processes. The bioinformatics analysis confirmed the differential expression of GA2, GA3, and GA20 gibberellin oxidase genes (VvGA2oxs, VvGA3oxs, and VvGA20oxs) in the grape genome, and laid a theoretical basis for exploring its role in grape. Based on the Arabidopsis GA2oxs, GA3oxs, and GA20oxs genes already reported, the VvGA2oxs, VvGA3oxs, and VvGA20oxs genes in the grape genome were identified using the BLAST software in the grape genome database. Bioinformatics analysis was performed using software such as DNAMAN v.5.0, Clustalx, MapGene2Chrom, MEME, GSDS v.2.0, ExPASy, DNAsp v.5.0, and MEGA v.7.0. Chip expression profiles were generated using grape Affymetrix GeneChip 16K and Grape eFP Browser gene chip data in PLEXdb. The expression of VvGA2oxs, VvGA3oxs, and VvGA20oxs gene families in stress was examined by qRT-PCR (Quantitative real-time-PCR). There are 24 GAoxs genes identified with the grape genome that can be classified into seven subgroups based on a phylogenetic tree, gene structures, and conserved Motifs in our research. The gene family has higher codon preference, while selectivity is negative selection of codon bias and selective stress was analyzed. The expression profiles indicated that the most of VvGAox genes were highly expressed under different time lengths of ABA (Abscisic Acid) treatment, NaCl, PEG and 5 °C. Tissue expression analysis showed that the expression levels of VvGA2oxs and VvGA20oxs in different tissues at different developmental stages of grapes were relatively higher than that of VvGA3oxs. Last but not least, qRT-PCR (Real-time fluorescent quantitative PCR) was used to determine the relative expression of the GAoxs gene family under the treatment of GA3 (gibberellin 3) and uniconazole, which can find that some VvGA2oxs was upregulated under GA3 treatment. Simultaneously, some VvGA3oxs and VvGA20oxs were upregulated under uniconazole treatment. In a nutshell, the GA2ox gene mainly functions to inactivate biologically active GAs, while GA20ox mainly degrades C20 gibberellins, and GA3ox is mainly composed of biologically active GAs. The comprehensive analysis of the three classes of VvGAoxs would provide a basis for understanding the evolution and function of the VvGAox gene family in a grape plant.

Genome-wide analysis of NAAT, DMAS, TOM, and ENA gene families in maize reveals their roles in regulating iron homeostasis

2020 ◽  
Author(s):  
Xin Zhang ◽  
Xiaojin Zhou ◽  
Suzhen Li ◽  
Jiaxing Huang ◽  
Sen Pang ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Iron Homeostasis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Mining ◽  
Gene Families ◽  
Pcr Analysis ◽  
Efflux Transporter ◽  
Iron Starvation ◽  
Maize Varieties

Abstract Background: Nicotianamine (NA) serves as not only the major chelator for iron transport but also the intermediate for synthesizing mugineic acid family phytosiderophores (MAs) which are secreted by graminaceous plants for Fe uptake. Therefore, the production and secretion of MAs are key steps for maintaining iron homeostasis in plants. Nicotianamine aminotransferase (NAAT), 2’-deoxymugineic acid synthase (DMAS), MAs efflux transporter (TOM), and efflux transporter of NA (ENA) were identified to be involved in these processes in rice and barley, whereas little systematic study has been performed in maize (Zea mays.L). Results: Here, we identified five ZmNAAT, nine ZmDMAS, eleven ZmTOM, and two ZmENA genes in maize by genome mining. RNA-sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) analysis revealed that the expression of these genes exhibited diverse tissue specificity and different responses to environmental iron conditions. Moreover, the expression patterns were related to their evolution relationships. In particular, the ZmNAAT family can be classified into two subgroups, with one group showed inhibited expression in root under iron excess status and another subclass were repressed in shoot under both iron deficiency and excess. Likewise, the expression of ZmDMAS1 was stimulated under iron deficiency, while the remaining genes fell into two sub-clades with different expression patterns. Significant up-regulation of ZmTOM1, ZmTOM3 and ZmENA1 were observed under iron starvation, while ZmTOM2 was induced under both iron-excess and deficiency. These results reflect changing demands for the synthesis and secretion of NA/MAs to balance iron homeostasis under fluctuating conditions. All the examined ZmNAAT and ZmDMAS proteins localized in cytoplasm, while plasma and tonoplast membrane, endomembrane, and vesicle localization were observed for ZmTOM and ZmENA proteins. These results indicate that ZmTOM and ZmENA proteins may contribute to not only intercellular export but also intracellular sequestration of NA and MAs to facilitate iron homeostasis. Conclusions: Our results suggest that different gene expression profiles and subcellular localization of ZmNAAT, ZmDMAS, ZmTOM, and ZmENA members may enable dedicate regulation of NA and phytosiderophores (PS) metabolism, shedding light on the understanding of iron-homeostasis in maize. Additionally, we also provided candidate genes for breeding iron-rich maize varieties.

scholarly journals Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Fu-Hao Lu ◽  
Neil McKenzie ◽  
Laura-Jayne Gardiner ◽  
Ming-Cheng Luo ◽  
Anthony Hall ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hexaploid Wheat ◽  
Aegilops Tauschii ◽  
Wheat Chromosome ◽  
Pilot Scale ◽  
Chromatin Accessibility ◽  
Diploid Progenitor ◽  
Genomic Changes ◽  
Chromosome Arm ◽  
Elevated Expression

Abstract Background Polyploidy is centrally important in the evolution and domestication of plants because it leads to major genomic changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are not well understood. Results Using a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3 L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was ∼40% of the levels observed in diploid Ae tauschii. Several genes showed elevated expression during the later stages of grain development in wheat compared with Ae tauschii. Gene sequence and methylation differences probably accounted for only a few cases of differences in gene expression. In contrast, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression. Conclusions Our pilot-scale analyses show that chromatin compaction may orchestrate reduced gene expression levels in the hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm.

Construction and Characterization of a BAC Library of a Cold‐Tolerant Hexaploid Wheat Cultivar

Crop Science ◽  
2005 ◽  
Vol 45 (4) ◽  
pp. 1571-1577 ◽  
Author(s):  
Indira Ratnayaka ◽  
Monica Båga ◽  
D. Brian Fowler ◽  
Ravindra N. Chibbar
Keyword(s):  
Hexaploid Wheat ◽  
Wheat Cultivar ◽  
Bac Library ◽  
Cold Tolerant

scholarly journals Transcriptome Analysis Reveals IsiA-Regulatory Mechanisms Underlying Iron Depletion and Oxidative-Stress Acclimation in Synechocystis sp. Strain PCC 6803

2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Yarui Cheng ◽  
Tianyuan Zhang ◽  
Li Wang ◽  
Wenli Chen
Keyword(s):  
Oxidative Stress ◽  
Network Analysis ◽  
Iron Deficiency ◽  
Regulatory Mechanisms ◽  
Functional Modules ◽  
Iron Stress ◽  
Iron Starvation ◽  
Stress Acclimation ◽  
And Oxidative Stress ◽  
Coexpression Network Analysis

ABSTRACT Microorganisms in nature are commonly exposed to various stresses in parallel. The isiA gene encodes an iron stress-induced chlorophyll-binding protein which is significantly induced under iron starvation and oxidative stress. Acclimation of oxidative stress and iron deficiency was investigated using a regulatory mutant of the Synechocystis sp. strain PCC 6803. In this study, the ΔisiA mutant grew more slowly in oxidative-stress and iron depletion conditions compared to the wild-type (WT) counterpart under the same conditions. Thus, we performed transcriptome sequencing (RNA-seq) analysis of the WT strain and the ΔisiA mutant under double-stress conditions to obtain a comprehensive view of isiA-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed significant differences between the WT strain and ΔisiA mutant, mainly related to photosynthesis and the iron-sulfur cluster. The deletion of isiA affects the expression of various genes that are involved in cellular processes and structures, such as photosynthesis, phycobilisome, and the proton-transporting ATPase complex. Weighted gene coexpression network analysis (WGCNA) demonstrated three functional modules in which the turquoise module was negatively correlated with superoxide dismutase (SOD) activity. Coexpression network analysis identified several hub genes of each module. Cotranscriptional PCR and reads coverage using the Integrative Genomics Viewer demonstrated that isiA, isiB, isiC, ssl0461, and dfp belonged to the isi operon. Three sRNAs related to oxidative stress were identified. This study enriches our knowledge of IsiA-regulatory mechanisms under iron deficiency and oxidative stress. IMPORTANCE This study analyzed the impact of isiA deletion on the transcriptomic profile of Synechocystis. The isiA gene encodes an iron stress-induced chlorophyll-binding protein, which is significantly induced under iron starvation. The deletion of isiA affects the expression of various genes that are involved in photosynthesis and ABC transporters. WGCNA revealed three functional modules in which the blue module was correlated with oxidative stress. We further demonstrated that the isi operon contained the following five genes: isiA, isiB, isiC, ssl0461, and dfp by cotranscriptional PCR. Three sRNAs were identified that were related to oxidative stress. This study enhances our knowledge of IsiA-regulatory mechanisms under iron deficiency and oxidative stress.

scholarly journals Key Function for the CCAAT-Binding Factor Php4 To Regulate Gene Expression in Response to Iron Deficiency in Fission Yeast

2008 ◽  
Vol 7 (3) ◽  
pp. 493-508 ◽  
Author(s):  
Alexandre Mercier ◽  
Stephen Watt ◽  
Jürg Bähler ◽  
Simon Labbé
Keyword(s):  
Iron Deficiency ◽  
Fission Yeast ◽  
Tricarboxylic Acid Cycle ◽  
Transcriptional Level ◽  
Mrna Levels ◽  
Gata Factor ◽  
Iron Starvation ◽  
A Genome ◽  
Binding Factor ◽  
Genes Encoding

ABSTRACT The fission yeast Schizosaccharomyces pombe responds to the deprivation of iron by inducing the expression of the php4 + gene, which encodes a negative regulatory subunit of the heteromeric CCAAT-binding factor. Once formed, the Php2/3/4/5 transcription complex is required to inactivate a subset of genes encoding iron-using proteins. Here, we used a pan-S. pombe microarray to study the transcriptional response to iron starvation and identified 86 genes that exhibit php4 + -dependent changes on a genome-wide scale. One of these genes encodes the iron-responsive transcriptional repressor Fep1, whose mRNA levels were decreased after treatment with the permeant iron chelator 2,2′-dipyridyl. In addition, several genes encoding the components of iron-dependent biochemical pathways, including the tricarboxylic acid cycle, mitochondrial respiration, amino acid biosynthesis, and oxidative stress defense, were downregulated in response to iron deficiency. Furthermore, Php4 repressed transcription when brought to a promoter using a yeast DNA-binding domain, and iron deprivation was required for this repression. On the other hand, Php4 was constitutively active when glutathione levels were depleted within the cell. Based on these and previous results, we propose that iron-dependent inactivation of Php4 is regulated at two distinct levels: first, at the transcriptional level by the iron-responsive GATA factor Fep1 and second, at the posttranscriptional level by a mechanism yet to be identified, which inhibits Php4-mediated repressive function when iron is abundant.

scholarly journals WITHDRAWN: Characterization and Expression Analysis of Gene Regulated by Iron Deficiency and Involved in Response to Auxin in

2016 ◽  
Author(s):  
Xiaoguang Li ◽  
Ying Gao ◽  
Yingli Li ◽  
Shuai Yan ◽  
Jianghong Zhang ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Expression Analysis

Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4

Genetica ◽  
2010 ◽  
Vol 138 (11-12) ◽  
pp. 1277-1296 ◽  
Author(s):  
Tong Geon Lee ◽  
Yong Jin Lee ◽  
Dae Yeon Kim ◽  
Yong Weon Seo
Keyword(s):  
Physical Mapping ◽  
Rice Chromosome ◽  
Wheat Chromosome ◽  
Chromosome 4 ◽  
Chromosome Arm
Sign in / Sign up

Export Citation Format

Share Document