scholarly journals Haplotype Diversity at the Pi-ta Locus in Cultivated Rice and Its Wild Relatives

2008 ◽  
Vol 98 (12) ◽  
pp. 1305-1311 ◽  
Author(s):  
X. Wang ◽  
Y. Jia ◽  
Q. Y. Shu ◽  
D. Wu
Keyword(s):  
Dna Sequences ◽  
Haplotype Diversity ◽  
Polymerase Chain Reaction Analysis ◽  
Single Amino Acid ◽  
Receptor Protein ◽  
Coding Region ◽  
Cultivated Rice ◽  
Genome Species ◽  
Rich Domain ◽  
Resistance Specificity

The Pi-ta gene in rice confers resistance to races of Magnaporthe oryzae that contain AVR-Pita. Pi-ta encodes a predicted cytoplasmic receptor protein with a nucleotide-binding site and a leucine-rich domain. A panel of 51 Oryza accessions of AA genome species Oryza sativa, O. glaberrima, O. rufipogon, O. nivara, and O. barthii, and CC genome species O. officinalis were sequenced to investigate the diversity present in the exon and intron regions of the Pi-ta gene. Two major clades were identified, consisting of 16 different sequences with numerous insertion and deletions. Only one Pi-ta resistance allele was identified despite DNA sequences revealing 16 Pi-ta variants. Most differences were identified in the intron region, and obvious selection of any motif was not observed in the coding region of Pi-ta variants. Reverse-transcription polymerase chain reaction analysis of seedlings revealed that all Pi-ta variants were expressed with or without pathogen inoculation. The 15 Pi-ta variants can be translated into nine proteins highly similar to the Pi-ta protein. Resistance to M. oryzae expressing AVR-Pita correlates with alanine and susceptibility correlates with serine at position 918 of Pi-ta in most accessions examined. These data confirm that a single amino acid controlling resistance specificity underlies the evolution of resistance of Pi-ta genes in rice.

scholarly journals Genetic polymorphism of the extracellular region in surface associated interspersed 1.1 gene of Plasmodium falciparum field isolates from Thailand

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Natpasit Chaianantakul ◽  
Tippawan Sungkapong ◽  
Jirapinya Changpad ◽  
Keawalin Thongma ◽  
Sasiwimon Sim-ut ◽  
...  
Keyword(s):  
Amino Acid ◽  
Dna Sequences ◽  
Balancing Selection ◽  
Haplotype Diversity ◽  
Research Area ◽  
Terminal Region ◽  
Common Amino Acid ◽  
Rich Domain ◽  
Extracellular Region ◽  
Variable Surface

Abstract Background A novel variable surface antigens (VSAs), Surface-associated interspersed proteins (SUFRINs), is a protein that is modified on the surface of infected red blood cell (iRBC). Modified proteins on the iRBC surface cause severe malaria, which can lead to death throughout the life cycle of a malaria parasite. Previous study suggested that SURFIN1.1 is an immunogenic membrane-associated protein which was encoded by using the surf1.1 gene expressed during the trophozoite and schizont stages. This study aimed to identify the regions of SURFIN1.1 and investigate the genetic diversity of the extracellular region of the surf1.1 gene. Methods A total of 32 blood samples from falciparum malaria cases that were diagnosed in Si Sa Ket Province, Thailand were collected. Plasmodium genomic DNA was extracted, and the extracellular region of surf1.1 gene was amplified using the polymerase chain reaction (PCR). A sequence analysis was then performed to obtain the number of haplotypes (H), the haplotype diversity (Hd), and the segregating sites (S), while the average number of nucleotide differences between two sequences (Pi); in addition, neutrality testing, Tajima’s D test, Fu and Li’s D* and F* statistics was also performed. Results From a total of 32 patient-isolated samples, 31 DNA sequences were obtained and analysed for surf1.1 gene extracellular region polymorphism. Researchers observed six distinct haplotypes in the current research area. Haplotype frequencies were 61.3%, 16.2%, and 12.9% for H1, H2, and H3, respectively. The remaining haplotype (H4-H6) frequency was 3.2% for each haplotype. Hd was 0.598 ± 0.089 with the Pi of 0.00381, and S was 15. The most common amino acid polymorphic site was E251Q; other sites included N48D, I49V, E228D, E235S, L265F, K267T, E276Q, and S288F. Fu and Li’s D* test value was − 1.24255, Fu and Li’s F* test value was − 1.10175, indicating a tendency toward negative balancing selection acting on the surf1.1 N-terminal region. The most polymorphic region was variable 2 (Var2) while cysteine-rich domain (CRD) was conserved in both the amino acid and nucleotide extracellular region of surf1.1 gene. Conclusions The Thai surf1.1 N-terminal region was well-conserved with only a few polymorphic sites remaining. In this study, the data regarding current bearing on the polymorphism of extracellular region of surf1.1 gene were reported, which might impact the biological roles of P. falciparum. In addition, may possibly serve as a suitable candidate for future development of SURFIN-based vaccines regarding malaria control. Graphic abstract

scholarly journals A Single-Amino-Acid Substitution in the TvbS1 Receptor Results in Decreased Susceptibility to Infection by Avian Sarcoma and Leukosis Virus Subgroups B and D and Resistance to Infection by Subgroup E In Vitro and In Vivo

2007 ◽  
Vol 82 (5) ◽  
pp. 2097-2105 ◽  
Author(s):  
Markéta Reinišová ◽  
Filip Šenigl ◽  
Xueqian Yin ◽  
Jiří Plachý ◽  
Josef Geryk ◽  
...  
Keyword(s):  
Cultured Cells ◽  
Genetic Defect ◽  
Single Amino Acid ◽  
Receptor Protein ◽  
Susceptibility To Infection ◽  
Rich Domain ◽  
Domain 3 ◽  
Avian Sarcoma

ABSTRACT The avian sarcoma and leukosis virus (ASLV) family of retroviruses contains five highly related envelope subgroups (A to E) thought to have evolved from a common viral ancestor in the chicken population. Three genetic loci in chickens determine the susceptibility or resistance of cells to infection by the subgroup A to E ASLVs. Some inbred lines of chickens display phenotypes that are somewhere in between either efficiently susceptible or resistant to infection by specific subgroups of ASLV. The tvb gene encodes the receptor for subgroups B, D, and E ASLVs. The wild-type TvbS1 receptor confers susceptibility to subgroups B, D, and E ASLVs. In this study, the genetic defect that accounts for the altered susceptibility of an inbred chicken line, line M, to infection by ASLV(B), ASLV(D), and ASLV(E) was identified. The tvb gene in line M, tvb r2 , encodes a mutant TvbS1 receptor protein with a substitution of a serine for a cysteine at position 125 (C125S). Here, we show that the C125S substitution in TvbS1 significantly reduces the susceptibility of line M cells to infection by ASLV(B) and ASLV(D) and virtually eliminates susceptibility to ASLV(E) infection both in cultured cells and in the incidence and growth of avian sarcoma virus-induced sarcomas in chickens. The C125S substitution significantly reduces the binding affinity of the TvbS1 receptor for the subgroup B, D, and E ASLV envelope glycoproteins. These are the first results that demonstrate a possible role of the cysteine-rich domain 3 in the function of the Tvb receptors.

scholarly journals Structure and chromosomal localization of the gene for the oligodendrocyte-myelin glycoprotein.

1990 ◽  
Vol 111 (6) ◽  
pp. 2673-2679 ◽  
Author(s):  
D D Mikol ◽  
M J Alexakos ◽  
C A Bayley ◽  
R S Lemons ◽  
M M Le Beau ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Neurofibromatosis Type ◽  
Genomic Clone ◽  
Chromosome 17 ◽  
Platelet Glycoprotein ◽  
Coding Region ◽  
Rich Domain ◽  
Leucine Rich Repeats ◽  
Flanking Regions ◽  
Oligodendrocyte Myelin Glycoprotein

Utilizing a cDNA clone encoding the oligodendrocyte-myelin glycoprotein (OMgp) to screen a human genomic DNA library, we have obtained a clone that contains the OMgp gene. The genomic clone was restriction mapped and the OMgp gene and its 5' and 3' flanking regions were sequenced. A single intron is found in the 5' untranslated region of the gene, while the coding region is uninterrupted by an intron. This placement of a single intron in the OMgp gene is identical to that of the gene for the alpha-chain of platelet glycoprotein Ib, which, along with OMgp, belongs to a family of proteins sharing two distinct structural domains: an NH2-terminal cysteine-rich domain and an adjacent domain of tandem leucine-rich repeats. Hence, it is possible that this family of proteins is not only related in terms of primary structure, but also through similar gene structure. Sequence comparison of the 5' and 3' flanking regions did not reveal striking similarities to other DNA sequences, and no obvious promoter elements were noted. By hybridization of the genomic clone to metaphase cells, we have localized the human OMgp gene to chromosome 17 bands q11-12, a region to which the neurofibromatosis type 1 gene has been previously mapped.

Identification of DNA sequences that regulate the expression of the Enterobacter cloacae UW4 1-aminocyclopropane-1-carboxylic acid deaminase gene

2000 ◽  
Vol 46 (12) ◽  
pp. 1159-1165 ◽  
Author(s):  
Varvara P Grichko ◽  
Bernard R Glick
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Dna Sequences ◽  
Regulatory Protein ◽  
Acc Deaminase ◽  
Enterobacter Cloacae ◽  
Receptor Protein ◽  
Protein Binding Site ◽  
Coding Region ◽  
Bacterial Strains

Analysis of the DNA sequence upstream of the previously isolated Enterobacter cloacae UW4 ACC deaminase gene (Shah et al. 1998) suggests that this segment contains several features that are thought to be involved in the transcriptional regulation of this gene. These features include half of a CRP (cAMP receptor protein) binding site, an FNR (fumarate-nitrate reduction) regulatory protein binding site, an LRP (leucine responsive regulatory protein) binding site, and an LRP-like protein coding region. ACC deaminase activity was measured following growth of either various Escherichia coli strains carrying a plasmid that contained the Enterobacter cloacae UW4 ACC deaminase gene, or of Enterobacter cloacae UW4. Variables that were compared include aerobic versus anaerobic conditions, the presence and absence of ACC in the growth medium, addition of leucine to the medium, and bacterial strains that did or did not contain either lrp or fnr genes. The data reported are consistent with the involvement of most, if not all, of the above mentioned potential regulatory regions in the expression of ACC deaminase.Key words: 1-aminocyclopropane-1-carboxylate, ACC, plant growth-promoting rhizobacteria, ACC deaminase, Enterobacter cloacae, leucine responsive regulatory protein.

Human DNA sequences homologous to a protein coding region conserved between homeotic genes of Drosophila

Cell ◽  
1984 ◽  
Vol 38 (3) ◽  
pp. 667-673 ◽  
Author(s):  
Michael Levine ◽  
Gerald M. Rubin ◽  
Robert Tjian
Keyword(s):  
Dna Sequences ◽  
Homeotic Genes ◽  
Coding Region ◽  
Protein Coding ◽  
Human Dna

scholarly journals Structural defects of a Pax8 mutant that give rise to congenital hypothyroidism

1999 ◽  
Vol 341 (1) ◽  
pp. 89-93 ◽  
Author(s):  
Gianluca TELL ◽  
Lucia PELLIZZARI ◽  
Gennaro ESPOSITO ◽  
Carlo PUCILLO ◽  
Paolo Emidio MACCHIA ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Congenital Hypothyroidism ◽  
Dna Sequences ◽  
Dna Interaction ◽  
Structural Defects ◽  
Molecular Defect ◽  
Wild Type ◽  
Coding Region ◽  
Induced Fit ◽  
Helical Content

Pax proteins are transcriptional regulators that play important roles during embryogenesis. These proteins recognize specific DNA sequences via a conserved element: the paired domain (Prd domain). The low level of organized secondary structure, in the free state, is a general feature of Prd domains; however, these proteins undergo a dramatic gain in α-helical content upon interaction with DNA (‘induced fit’). Pax8 is expressed in the developing thyroid, kidney and several areas of the central nervous system. In humans, mutations of the Pax8 gene, which are mapped to the coding region of the Prd domain, give rise to congenital hypothyroidism. Here, we have investigated the molecular defects caused by a mutation in which leucine at position 62 is substituted for an arginine. Leu62 is conserved among Prd domains, and contributes towards the packing together of helices 1 and 3. The binding affinity of the Leu62Arg mutant for a specific DNA sequence (the C sequence of thyroglobulin promoter) is decreased 60-fold with respect to the wild-type Pax8 Prd domain. However, the affinities with which the wild-type and the mutant proteins bind to a non-specific DNA sequence are very similar. CD spectra demonstrate that, in the absence of DNA, both wild-type Pax8 and the Leu62Arg mutant possess a low α-helical content; however, in the Leu62Arg mutant, the gain in α-helical content upon interaction with DNA is greatly reduced with respect to the wild-type protein. Thus the molecular defect of the Leu62Arg mutant causes a reduced capability for induced fit upon DNA interaction.

scholarly journals The association of CYP2D6 gene polymorphisms in the full-length coding region with higher recurrence rate of vivax malaria in Yunnan Province, China

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Herong Huang ◽  
Ying Dong ◽  
Yanchun Xu ◽  
Yan Deng ◽  
Canglin Zhang ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Gene Mutation ◽  
Dna Sequences ◽  
Vivax Malaria ◽  
Yunnan Province ◽  
Reference Sequence ◽  
Radical Cure ◽  
Coding Region ◽  
Cyp2d6 Gene ◽  
Genotype 4

Abstract Background Accumulating evidence suggest that compromised CYP2D6 enzyme activity caused by gene mutation could contribute to primaquine failure for the radical cure of vivax malaria. The current study aims to preliminarily reveal the association between the recurrence of vivax malaria in Yunnan Province and CYP2D6 gene mutation by analysing polymorphisms in the entire coding region of human CYP2D6 gene. Methods Blood samples were collected from patients with vivax malaria, who received "chloroquine and 8-day course of primaquine therapy" in Yunnan Province. The suspected relapsed cases were determined by epidemiological approaches and gene sequence alignment. PCR was conducted to amplify the CYP2D6 gene in the human genome, and the amplified products were then sequenced to compare with the non-mutation “reference” sequence, so as to ensure correct sequencing results and to determine 9 exon regions. Subsequently, the DNA sequences of 9 exons were spliced into the coding DNA sequence (CDS), which, by default, is known as maternal CDS. The paternal CDS was obtained by adjusting the bases according to the sequencing peaks. The mutation loci, haplotypes (star alleles), genotypes and odds ratios (OR) of all the CDSs were analysed. Results Of the119 maternal CDS chains in total with 1491 bp in length, 12 mutation sites in the 238 maternal and paternal CDS chains were detected. The c.408G > C mutation was most frequently detected in both suspected relapsed group (SR) and non-relapsed group (NR), reaching 85.2% (75/88) and 76.0% (114/150), respectively. The c.886C > T mutation was most closely related to the recurrence of vivax malaria (OR = 2.167, 95% CI 1.104–4.252, P < 0.05). Among the 23 haplotypes (Hap_1 ~ Hap_23), Hap_3 was non-mutant, and the sequence structure of Hap_9 was the most complicated one. Five star alleles, including *1, *2, *4, *10 and *39, were confirmed by comparison, and CYP2D6*10 allele accounted for the largest percentage (45.4%, 108/238). The frequency of CYP2D6*2 allele in the SR group was significantly higher than that in the NR group (Χ2 = 16.177, P < 0.05). Of the defined 24 genotypes, 8 genotypes, including *4/*4, *4/*o, *2/*39, *39/*m, *39/*x, *1/*r, *1/*n, and *v/*10, were detected only in the SR group. Conclusion Mutation of CYP2D6*10 allele accounts for the highest proportion of vivax malaria cases in Yunnan Province. The mutations of c. 886C > T and CYP2D6*2 allele, which correspond to impaired PQ metabolizer phenotype, are most closely related to the relapse of vivax malaria. In addition, the genotype *4/*4 with null CYP2D6 enzyme function was only detected in the SR group. These results reveal the risk of defected CYP2D6 enzyme activity that diminishes the therapeutic effect of primaquine on vivax malaria.

Multiple calmodulin mRNA species are derived from two distinct genes

1987 ◽  
Vol 7 (5) ◽  
pp. 1873-1880
Author(s):  
H Nojima ◽  
K Kishi ◽  
H Sokabe
Keyword(s):  
Dna Sequences ◽  
Northern Blotting ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Rat Tissues ◽  
Coding Region ◽  
Genomic Libraries ◽  
Mrna Species ◽  
Nuclease Mapping ◽  
Rat Genome

We have observed three calmodulin mRNA species in rat tissues. In order to know from how many expressed genes they are derived, we have investigated the genomic organization of calmodulin genes in the rat genome. From a rat brain cDNA library, we obtained two kinds of cDNAs (pRCM1 and pRCM3) encoding authentic calmodulin. DNA sequence analysis of these cDNA clones revealed substitutions of nucleotides at 73 positions of 450 nucleotides in the coding region, although the amino acid sequences of these calmodulins are exactly the same. DNA sequences in the 5' and 3' noncoding regions are quite different between these two cDNAs. From these results, we conclude that they are derived from two distinct bona fide calmodulin genes, CaMI (pRCM1) and CaMII (pRCM3). Total genomic Southern hybridization suggested four distinct calmodulin-related genes in the rat genome. By cloning and sequencing the calmodulin-related genes from rat genomic libraries, we demonstrated that the other two genes are processed pseudogenes generated from the CaMI (lambda SC9) and CaMII (lambda SC8) genes, respectively, through an mRNA-mediated process of insertions. Northern blotting showed that the CaMI gene is transcribed in liver, muscle, and brain in similar amounts, whereas the CaMII gene is transcribed mainly in brain. S1 nuclease mapping indicated that the CaMI gene produced two mRNA species (1.7 and 4 kilobases), whereas the CaMII gene expressed a single mRNA species (1.4 kilobases).

Identification of the principal promoter sequence of the c-H-ras transforming oncogene: deletion analysis of the 5'-flanking region by focus formation assay

1987 ◽  
Vol 7 (8) ◽  
pp. 2933-2940
Author(s):  
H Honkawa ◽  
W Masahashi ◽  
S Hashimoto ◽  
T Hashimoto-Gotoh
Keyword(s):  
Dna Sequences ◽  
Promoter Sequence ◽  
Ras Oncogene ◽  
Coding Region ◽  
Focus Formation ◽  
S1 Nuclease ◽  
Protein Coding ◽  
Consensus Sequences ◽  
Flanking Region ◽  
Virus C

A number of deletion mutants were isolated, including 5', 3', and internal deletions in the 5'-flanking region of the human cellular oncogene related to the Harvey sarcoma virus (c-H-ras), and their transforming activities were examined in NIH 3T3 cells. DNA sequences which could not be detected without losing transforming activity were localized to a relatively short stretch upstream of the region which showed homology to the 5'-flanking region of v-H-ras oncogene. S1 nuclease analysis indicated that there were two clusters of mRNA start sites at positions that were about 1,371 and 1,298 base pairs upstream of the first coding ATG. The minimum region required for promoter function was estimated to be a 51-base-pair-long (or less) DNA segment. The promoter was GC rich (78%) and did not contain the consensus sequences that are usually observed in PolII-directed promoters but contained a GC box within which one of the mRNA start sites was included. In addition, two sets of positive and negative elements seemed to be located between the promoter and the protein-coding region, which appeared to influence positively and negatively, respectively, the efficiency of transformation with the c-H-ras oncogene.

scholarly journals Phylogeography of Bulinus truncatus (Audouin, 1827) (Gastropoda: Planorbidae) in Selected African Countries

2018 ◽  
Vol 3 (4) ◽  
pp. 127 ◽  
Author(s):  
Eniola Abe ◽  
Yun-Hai Guo ◽  
Haimo Shen ◽  
Masceline Mutsaka-Makuvaza ◽  
Mohamed Habib ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Haplotype Diversity ◽  
Snail Host ◽  
Snail Species ◽  
African Countries ◽  
Urinary Schistosomiasis ◽  
Bulinus Truncatus ◽  
High Haplotype Diversity ◽  
Gene Coi ◽  
Mitochondrial Cytochrome Oxidase

The transmission of some schistosome parasites is dependent on the planorbid snail hosts. Bulinus truncatus is important in urinary schistosomiasis epidemiology in Africa. Hence, there is a need to define the snails’ phylogeography. This study assessed the population genetic structure of B. truncatus from Giza and Sharkia (Egypt), Barakat (Sudan) and Madziwa, Shamva District (Zimbabwe) using mitochondrial cytochrome oxidase subunit 1 gene (COI) and internal transcribed spacer 1 (ITS 1) markers. COI was sequenced from 94 B. truncatus samples including 38 (Egypt), 36 (Sudan) and 20 (Zimbabwe). However, only 51 ITS 1 sequences were identified from Egypt (28) and Sudan (23) (because of failure in either amplification or sequencing). The unique COI haplotypes of B. truncatus sequences observed were 6, 11, and 6 for Egypt, Sudan, and Zimbabwe, respectively. Also, 3 and 2 unique ITS 1 haplotypes were observed in sequences from Egypt and Sudan respectively. Mitochondrial DNA sequences from Sudan and Zimbabwe indicated high haplotype diversity with 0.768 and 0.784, respectively, while relatively low haplotype diversity was also observed for sequences from Egypt (0.334). The location of populations from Egypt and Sudan on the B. truncatus clade agrees with the location of both countries geographically. The clustering of the Zimbabwe sequences on different locations on the clade can be attributed to individuals with different genotypes within the population. No significant variation was observed within B. truncatus populations from Egypt and Sudan as indicated by the ITS 1 tree. This study investigated the genetic diversity of B. truncatus from Giza and Sharkia (Egypt), Barakat area (Sudan), and Madziwa (Zimbabwe), which is necessary for snail host surveillance in the study areas and also provided genomic data of this important snail species from the sampled countries.

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