Characterization of Salt Overly Sensitive 1 (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd.)

Genome ◽  
2009 ◽  
Vol 52 (7) ◽  
pp. 647-657 ◽  
Author(s):  
P. J. Maughan ◽  
T. B. Turner ◽  
C. E. Coleman ◽  
D. B. Elzinga ◽  
E. N. Jellen ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Dna Sequences ◽  
Genomic Sequence ◽  
Chenopodium Quinoa ◽  
Fish Analysis ◽  
Cdna Sequences ◽  
Grain Crop ◽  
High Level ◽  
Salt Overly Sensitive

Salt tolerance is an agronomically important trait that affects plant species around the globe. The Salt Overly Sensitive 1 (SOS1) gene encodes a plasma membrane Na+/H+ antiporter that plays an important role in germination and growth of plants in saline environments. Quinoa (Chenopodium quinoa Willd.) is a halophytic, allotetraploid grain crop of the family Amaranthaceae with impressive nutritional content and an increasing worldwide market. Many quinoa varieties have considerable salt tolerance, and research suggests quinoa may utilize novel mechanisms to confer salt tolerance. Here we report the cloning and characterization of two homoeologous SOS1 loci (cqSOS1A and cqSOS1B) from C. quinoa, including full-length cDNA sequences, genomic sequences, relative expression levels, fluorescent in situ hybridization (FISH) analysis, and a phylogenetic analysis of SOS1 genes from 13 plant taxa. The cqSOS1A and cqSOS1B genes each span 23 exons spread over 3477 bp and 3486 bp of coding sequence, respectively. These sequences share a high level of similarity with SOS1 homologs of other species and contain two conserved domains, a Nhap cation-antiporter domain and a cyclic-nucleotide binding domain. Genomic sequence analysis of two BAC clones (98 357 bp and 132 770 bp) containing the homoeologous SOS1 genes suggests possible conservation of synteny across the C. quinoa sub-genomes. This report represents the first molecular characterization of salt-tolerance genes in a halophytic species in the Amaranthaceae as well as the first comparative analysis of coding and non-coding DNA sequences of the two homoeologous genomes of C. quinoa.

Characterization of equine cDNA sequences for αS1-, β- and κ-casein

2003 ◽  
Vol 70 (1) ◽  
pp. 29-36 ◽  
Author(s):  
Tina Lenasi ◽  
Irena Rogelj ◽  
Peter Dovc
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Genomic Region ◽  
Interspecies Comparison ◽  
Cryptic Exon ◽  
Conserved Sequence ◽  
Cdna Sequences ◽  
Sequence Identity ◽  
Lactating Mammary Gland

Here we report the entire cDNA sequences for equine αS1-, β- and κ-casein. Based on interspecies comparison, nine exons were found in equine β-casein and five in κ-casein. In equine αS1-casein cDNA the exon 5 was missing, which resulted in the total of 18 exons instead of 19 theoretically possible exons in αS1-casein cDNA. Comparison of DNA sequences representing exon 5 in other species with corresponding equine genomic region confirmed the presence of cryptic exon in horse genomic DNA. Equine αS1-casein mRNA was present in three forms in the lactating mammary gland and we showed that the two shorter forms were produced by skipping either the exon 8 or exon 15. In horse, as in some other mammals, β- and κ-casein are considerably more conserved (sequence identity 53% to 59% and 57% to 67%, respectively) than αS1-casein which appears as the most variable casein among species (sequence identity 40% to 54%). Interestingly, horse caseins resemble human much more than bovine caseins which may also explain the high dietetic value of mares' milk.

Cloning and characterization of an alternative splicing transcript of the gene coding for human cytidine deaminase

2007 ◽  
Vol 85 (1) ◽  
pp. 96-102 ◽  
Author(s):  
Bianca Cristina Garcia Lisboa ◽  
Tamara da Rocha Machado ◽  
Daniel Carvalho Pimenta ◽  
Sang Won Han
Keyword(s):  
Alternative Splicing ◽  
Dna Sequences ◽  
Genomic Sequence ◽  
Cytidine Deaminase ◽  
Alternative Form ◽  
Nih3t3 Cells ◽  
Reading Frame ◽  
Gene Coding ◽  
Identification And Characterization

Human cytidine deaminase (HCD) catalyzes the deamination of cytidine or deoxycytidine to uridine or deoxyuridine, respectively. The genomic sequence of HCD is formed by 31 kb with 4 exons and several alternative splicing signals, but an alternative form of HCD has yet to be reported. Here we describe the cloning and characterization of a small form of HCD, HSCD, and it is likely to be a product of alternative splicing of HCD. The alignment of DNA sequences shows that the HSCD matches HCD in 2 parts, except for a deletion of 170 bp. Based on the HCD genome organization, exons 1 and 4 should be joined and all sequences of introns and exons 2 and 3 should be deleted by splicing. This alternative splicing shifted the translation of the reading frame from the point of splicing. The estimated molecular mass is 9.8 kDa, and this value was confirmed by Western blot and mass spectroscopy after expressing the gene fused with glutathionine-S-transferase in the pGEX vector. The deletion and shift of the reading frame caused a loss of HCD activity, which was confirmed by enzyme assay and also with NIH3T3 cells modified to express HSCD and challenged against cytosine arabinoside. In this work we describe the identification and characterization of HSCD, which is the product of alternative splicing of the HCD gene.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 710-717 ◽  
Author(s):  
B. Kolano ◽  
B.W. Gardunia ◽  
M. Michalska ◽  
A. Bonifacio ◽  
D. Fairbanks ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chenopodium Quinoa ◽  
5S Rdna ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Rdna Loci

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18–24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18–24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12–13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12–13P was very similar to GISH results, suggesting that the 12–13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

Isolation and characterization of the rye Waxy gene

Genome ◽  
2009 ◽  
Vol 52 (7) ◽  
pp. 658-664 ◽  
Author(s):  
Jie Xu ◽  
Michele Frick ◽  
André Laroche ◽  
Zhong-Fu Ni ◽  
Bao-Yun Li ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Evolutionary Relationship ◽  
Waxy Gene ◽  
Coding Region ◽  
Gene Encoding ◽  
Sequence Comparisons ◽  
Cdna Sequences ◽  
Isolation And Characterization ◽  
Complete Genomic

Complete genomic and cDNA sequences of the Waxy gene encoding granule-bound starch synthase I (GBSSI) were isolated from the rye genome and characterized. The full-length rye Waxy genomic DNA and cDNA are 2767 bp and 1815 bp, respectively. The genomic sequence has 11 exons interrupted by 10 introns. The rye Waxy gene is GC-rich, with a higher GC frequency in the coding region, especially in the third position of the codons. Exon regions of the rye Waxy gene are more conserved than intron regions when compared with the homologous sequences of other cereals. The mature rye GBSSI proteins share more than 95% sequence identity with their homologs in wheat and barley. A phylogenetic tree based on sequence comparisons of available plant GBSSI proteins shows the evolutionary relationship among Waxy genes from rye and other plant genomes. The identification of the rye Waxy gene will enable the manipulation of starch metabolism in rye and triticale.

scholarly journals Identification and Characterization of Carbendazim-Resistant Isolates of Gibberella zeae

Plant Disease ◽  
2010 ◽  
Vol 94 (9) ◽  
pp. 1137-1142 ◽  
Author(s):  
Xin Liu ◽  
Yanni Yin ◽  
Jianbing Wu ◽  
Jinhua Jiang ◽  
Zhonghua Ma
Keyword(s):  
Point Mutation ◽  
Dna Sequences ◽  
Mycelial Growth ◽  
Point Mutations ◽  
Gibberella Zeae ◽  
Allele Specific ◽  
High Level ◽  
Polymerase Chain Reaction Primers ◽  
Moderately Resistant

Sensitivity of Gibberella zeae to carbendazim was determined by measuring mycelial growth in fungicide-amended media. Among 1,529 isolates tested, 31 isolates showed a high level of resistance (HR) to carbendazim (fungicide concentration that results in 50% inhibition of mycelial growth [EC50] of 10.35 to 30.26 mg a.i. liter–1) and 10 isolates were moderately resistant (MR) (EC50 of 4.50 to 7.28 mg a.i. liter–1). The remaining 1,488 isolates were sensitive to carbendazim and were unable to grow on potato dextrose agar amended with carbendazim at 2 mg a.i. liter–1. Analysis of DNA sequences of the β2-tubulin (Tub2) gene showed that all 10 MR isolates had a point mutation at codon 198 causing a replacement of glutamic acid by glutamine. At the codon position 167, the amino acid phenylalanine was replaced by tyrosine in 28 of 31 HR isolates. The remaining three HR isolates had a point mutation at codon 200 which converted phenylalanine to tyrosine. Based on these point mutations in the Tub2 gene, allele-specific polymerase chain reaction primers were developed for rapid detection of the point mutations. The rapid molecular method will be a valuable tool for the monitoring of carbendazim resistance in G. zeae. Additionally, deletion of the β1-tubulin gene (Tub1) in the HR isolate GJ33 resulted in increased resistance to carbendazim. These results indicate that Tub1 plays a role in the sensitivity of G. zeae to carbendazim.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

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