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See detailComparative analysis of two sister Erythrophleum species (Leguminosae) reveal contrasting transcriptome-wide responses to early drought stress
Neji, M.; Gorel, Anaïs ULiege; Ojeda, D. I. et al

in Gene (2019), 694

With the ongoing climate change, African rainforests are expected to experience severe drought events in the future. In Africa, the tropical genus Erythrophleum (Fabaceae) includes two forest sister ... [more ▼]

With the ongoing climate change, African rainforests are expected to experience severe drought events in the future. In Africa, the tropical genus Erythrophleum (Fabaceae) includes two forest sister timber tree species displaying contrasting geographical distributions. Erythrophleum ivorense is adapted to wet evergreen Guineo-Congolian forests, whereas E. suaveolens occurs in a wider range of climates, being found in moist dense forests but also in gallery forests under a relatively drier climate. This geographical distribution pattern suggests that the two species might cope differently to drought at the genomic level. Yet, the genetic basis of tolerance response to drought stress in both species is still uncharacterized. To bridge this gap, we performed an RNA-seq approach on seedlings from each species to monitor their transcriptional responses at different levels of drought stress (0, 2 and 6 weeks after stopping watering seedlings). Monitoring of wilting symptoms revealed that E. suaveolens displayed an earlier phenotypic response to drought stress than E. ivorense. At the transcriptomic level, results revealed 2020 (1204 down-regulated/816 up-regulated) and 1495 differentially expressed genes (DEGs) in response to drought stress from a total of 67,432 and 66,605 contigs assembled in E. ivorense and E. suaveolens, respectively. After identifying 30,374 orthologs between species, we found that only 7 of them were DEGs shared between species, while 587 and 458 were differentially expressed only in E. ivorense or E. suaveolens, respectively. GO and KEGG enrichment analysis revealed that the two species differ in terms of significantly regulated pathways as well as the number and expression profile of DEGs (Up/Down) associated with each pathway in the two stress stages. Our results suggested that the two studied species react differently to drought. E. suaveolens seems displaying a prompt response to drought at its early stage strengthened by the down-regulation of many DEGs encoding for signaling and metabolism-related pathways. A considerable up-regulation of these pathways was also found in E. ivorense at the late stage of drought, suggesting this species may be a late responder. Overall, our data may serve as basis for further understanding the genetic control of drought tolerance in tropical trees and favor the selection of crucial genes for genetically enhancing drought resistance. © 2019 Elsevier B.V. [less ▲]

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See detailGenome-wide characterization and expression analysis of the aldehyde dehydrogenase (ALDH) gene superfamily under abiotic stresses in cotton
Xinlei, Guo; Yuanyuan, Wang; Lu, Hejun ULiege

in Gene (2017)

In plants, aldehyde dehydrogenases (ALDHs) function as ‘aldehyde scavengers’ by removing reactive aldehydes and thus play important roles in stress responses. To date, 30 ALDHs have been identified in ... [more ▼]

In plants, aldehyde dehydrogenases (ALDHs) function as ‘aldehyde scavengers’ by removing reactive aldehydes and thus play important roles in stress responses. To date, 30 ALDHs have been identified in Gossypium raimondii, whereas ALDHs have not been studied in Gossypium arboreum or in tetraploid cotton. In this study, we identified 30, 59 and 59 aldehyde dehydrogenase (ALDH) genes from G. arboreum, G. hirsutum and G. barbadense, re- spectively. Gene structure analysis revealed that members of the same family exhibit similar exon–intron structures and structural domains, and all members of the ALDH18 family possess a distinct AA-kinase domain. Synteny analysis showed that segmental and tandem duplications have played an important role in the ex- pansion and evolution of ALDHs in cotton. Phylogenetic and synteny analysis between G. arboreum and G. raimondii demonstrated that all GaALDHs and GrALDHs are orthologous and that most GaALDHs are located in syntenic blocks corresponding to those of G. raimondii, implying that these genes appeared before the divergence of G. arboreum and G. raimondii and that no expansion of the ALDH superfamily has occurred in these two cotton species. Quantitative real-time PCR analysis revealed that the majority of GaALDHs and GhALDHs are up- regulated under conditions of high salinity and drought, indicating that these genes may be stress responsive. The findings of this study, based on genome-wide identification of ALDHs in Gossypium and analysis of their evolution and expression, provide a foundation for further analysis of ALDHs and suggest potential target genes for improving stress resistance in cotton. [less ▲]

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See detailAnalysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods
Satish, Lakkakula; Shilpha, Jayabalan; Pandian, Subramani et al

in Gene (2015), 576

Genetic variation among 45 genotypes of sorghum (Sorghum bicolor L.) representing seven subpopulations was assessed using three single primer amplification reaction (SPAR) methods viz., inter-simple ... [more ▼]

Genetic variation among 45 genotypes of sorghum (Sorghum bicolor L.) representing seven subpopulations was assessed using three single primer amplification reaction (SPAR) methods viz., inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD) and directed amplification of minisatellite-region DNA (DAMD). Totally 15 ISSR, 8 RAPD and 7 DAMD primers generated 263 amplification products, accounting for 84.6% polymorphism across all the genotypes. The Mantel's test of correlation revealed the best correlation between ISSR and cumulative data with a correlation coefficient (r) of 0.84. Assessment of population diversity indicated that the maximum intra population genetic diversity was recorded among high FeZn lines (HFL) having maximum values of Nei's genetic diversity (h) (0.244), Shannon information index (I) (0.368) and the percentage of polymorphic loci (Pp) (72.65%) while the corresponding lowest values of 0.074, 0.109 and 17.95% respectively were observed among the members of MDT subpopulation. The mean coefficient of gene differentiation (GST) and the gene flow (Nm) between populations were observed to be 0.396 and 0.7680 respectively. The analysis of molecular variance (AMOVA) suggested that maximum genetic variation exists within populations (95%) than among populations (5%). Thus the information obtained from this study could be utilized in sorghum breeding programmes for the development of varieties with improved nutrition and agronomic values in future. [less ▲]

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See detailScreening for the presence of FMR1 premutation alleles in women with fibromyalgia.
Rodriguez-Revenga, Laia; Madrigal, Irene; Blanch-Rubio, Josep et al

in Gene (2013), 512(2), 305-8

Fibromyalgia is a chronic condition characterized by widespread pain, fatigue, non-restorative sleep and cognitive difficulties that affects 2-4% of the general population. Recently a possible ... [more ▼]

Fibromyalgia is a chronic condition characterized by widespread pain, fatigue, non-restorative sleep and cognitive difficulties that affects 2-4% of the general population. Recently a possible relationship between the FMR1 premutation and fibromyalgia has been pointed out. In attempt to gather more data we screened for the FMR1 CGG expansion 700 DNA samples from unrelated fibromyalgia patients. This data might be useful for evaluating the incorporation of this test in rheumatologic procedures for women with fibromyalgia. The observed frequency of FMR1 premutation carriers (3 of 700, 0.4%) is not significantly different from the estimated rate in the general female population (1/250-1/400) (P=0.539, P=0.716). Clinical examination of the FMR1 premutation carriers identified revealed that all of them had important neurological symptoms with regard to muscular symptoms, neurocognitive alterations and neurovegetative impairments. With regard to other clinical aspects of the disease the cases apparently did not differ from the average fibromyalgia patients. On the basis of our results an FMR1 screening among fibromyalgia female patients would not be recommended. However it would be worthwhile to further evaluate the different clinical presentations that fibromyalgia patients might present based on their FMR1 premutation carrier status. [less ▲]

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See detailEvidence of association between interferon regulatory factor 5 gene polymorphisms and asthma.
Wang, Chuan; Rose-Zerilli, Matthew J.; Koppelman, Gerard H. et al

in Gene (2012), 504(2), 220-5

Asthma is a heterogeneous disorder hallmarked by chronic inflammation in the respiratory system. Exacerbations of asthma are correlated with respiratory infections. Considering the implication of ... [more ▼]

Asthma is a heterogeneous disorder hallmarked by chronic inflammation in the respiratory system. Exacerbations of asthma are correlated with respiratory infections. Considering the implication of interferon regulatory factor 5 (IRF5) in innate and adaptive immunity, we investigated the preferential transmission patterns of ten IRF5 gene polymorphisms in two asthmatic family cohorts. A common IRF5 haplotype was found to be associated with asthma and the severity of asthmatic symptoms. Stratified analysis of subgroups of asthmatic individuals revealed that the associations were more pronounced in nonatopic asthmatic individuals. In addition, the risk alleles of IRF5 polymorphisms for asthma were almost completely opposite to those for autoimmune disorders. Our study provides the first evidence of association between IRF5 and asthma, and sheds light on the related but potentially distinct roles of IRF5 alleles in the pathogenesis of asthma and autoimmune disorders. [less ▲]

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See detailMolecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers (SSR)
Hasnaoui, Nejib ULiege; Buonamici, Anna; Sebastiani, Federico et al

in Gene (2012)

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about ... [more ▼]

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In the present study, we report the development of 4 new polymorphic SSR markers. They have been used in addition to 11 SSRs previously published to investigate molecular diversity of 33 Punica granatum ecotypes. Based on the multi-locus profiles, twenty-two distinctive genotypes were identified. Globally, quite low genetic diversity has been revealed, as measured by allele richness (2.83 per locus) and heterozygosity (He = 0.245; Ho = 0.243), reflecting the narrow genetic background of the plant material. Four synonymous groups could be detected involving 15 accessions. Results of ordination and cluster analysis suggested that almost all the Tunisian cultivars share similar genetic background, and are likely derived from a small number of introductions in ancient times. Results issued from this study provide essential information to project a previous termpomegranatenext term core-collection without plant material duplication and for sustainable management of previous termpomegranatenext term landraces at national and international level. Furthermore, these SSR markers are powerful tool for marker assisted selection (MAS) program and for QTL studies. [less ▲]

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See detailRole of myo-inositol phosphate synthase and sucrose synthase genes in plant seed development
Abid, Ghassen ULiege; Baudoin, Jean-Pierre ULiege; Muhovski, Yordan et al

in Gene (2009), 439

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See detailIdentification and characterization of four splicing variants of ovine POUF1 gene
Bastos, Estella; Avila, S.; Cravador, Alfredo et al

in Gene (2006), 382

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See detailSecreted subtilisin gene family in Trichophyton rubrum
Jousson, O.; Lechenne, B.; Bontems, O. et al

in Gene (2004), 339

Secreted proteases constitute potential virulence factors of dermatophytes. A total of seven genes encoding putative serine proteases of the subtilisin family (SUB) were isolated in Trichophyton rubrum ... [more ▼]

Secreted proteases constitute potential virulence factors of dermatophytes. A total of seven genes encoding putative serine proteases of the subtilisin family (SUB) were isolated in Trichophyton rubrum. Based on sequence data and intron-exon structure, a phylogenetic analysis of subtilisins from T rubrum and other fungi revealed a presumed ancestral lineage comprising T rubrum SUB2 and Aspergillus SUBs. All other SUBs (SUB1, SUB3-7) are dermatophyte-specific and have apparently emerged more recently, through successive gene duplication events. We showed that two subtilisins, Sub3 and Sub4, were detected in culture supernatants of T rubrum grown in a medium containing soy protein as a sole nitrogen source. Both recombinant enzymes produced in Pichia pastoris are highly active on keratin azure suggesting that these proteases play an important role in invasion of keratinised tissues by the fungus. The set of deduced amino acid sequences of T rubrum SUB ORFs allowed the identification of orthologous Subs secreted by other dermatophyte species using proteolysis and mass spectrometry. (C) 2004 Elsevier B.V. All rights reserved. [less ▲]

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See detailMolecular cloning and characterisation of the CD18 partner in ovine (Ovis aries) beta(2)-integrins
Zecchinon, Laurent ULiege; Fett, Thomas ULiege; Baise, Etienne ULiege et al

in Gene (2004), 334

The leukocyte integrins play a critical role in a number of cellular adhesive interactions during the immune response. We describe here the isolation and characterization of the ovine beta(2) (CD18 ... [more ▼]

The leukocyte integrins play a critical role in a number of cellular adhesive interactions during the immune response. We describe here the isolation and characterization of the ovine beta(2) (CD18) subunit, common to the leukocyte beta(2)-integrin family. The deduced 770-amino-acid sequence reveals a transmembrane protein with 81%, 83% and 95% identity with its murine, human and bovine homologues, respectively. Comparisons of CD18 sequences emphasize the functional importance of the beta(2) subunit I-like domain and included metal ion-dependent adhesion site (MIDAS)-like motif and confirm that of the cytoplasmic tail. The data provided here will offer the possibility to explore new avenues in studies based on the ovine model. (C) 2004 Elsevier B.V. All rights reserved. [less ▲]

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See detailGenomic structure, organisation, and promoter analysis of the bovine (Bos taurus) Mx1 gene
Gérardin; Baise, Etienne ULiege; Pire, Grégory et al

in Gene (2004), 326

Some MX proteins are known to confer a specific resistance against a panel of single-stranded RNA viruses. Many diseases due to such viruses are known to affect cattle worldwide, raising the possibility ... [more ▼]

Some MX proteins are known to confer a specific resistance against a panel of single-stranded RNA viruses. Many diseases due to such viruses are known to affect cattle worldwide, raising the possibility that the identification of an antiviral isoform of a bovine MX protein would allow the implementation of genetic selection programs aimed at improving innate resistance of cattle. With this potential application in mind, the present study was designed to isolate the bovine Mx1 gene including its promoter region and to investigate its genomic organisation and promoter reactivity. The bovine Mx1 gene is made up of 15 exons. All exon-intron boundaries conformed to the consensus sequences. A PCR product that contained a approximately 1-kb, 5'-flanking region upstream from the putative transcription start site was sequenced. Unexpectedly, this DNA region did not contain TATA or CCAAT motifs. A computer scan of the region disclosed a series of putative binding sites for known cytokines and transcription factors. There was a GAAAN(1-2)GAAA(C/G) motif, typical of an interferon-sensitive responsive element, between -118 and -107 from the putative transcription start site. There were also a NF-kappaB, two interleukin-6 binding sites, two Sp1 sites and five GC-rich boxes. The region also contained 12 stretches of the GAAA type, as described in all IFN-inducible genes. Bovine Mx1 expression was assessed by Northern blotting and immunofluorescence in the Madin Darby bovine kidney cells (MDBK) cell line treated with several stimuli. In conclusion, the bovine Mx1 gene and promoter region share the major structural and functional characteristics displayed by their homologs described in the rainbow trout, chicken, mouse and man. [less ▲]

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See detailThe bovine (Bos taurus) CD11a-encoding cDNA: molecular cloning, characterisation and comparison with the human and murine glycoproteins
Fett, Thomas ULiege; Zecchinon, Laurent ULiege; Baise, Etienne ULiege et al

in Gene (2004), 325

The bovine cDNA encoding CD11 a cell-surface glycoprotein involved in multiple leukocyte functions, was sequenced and compared with the human and murine sequences. Despite some focal differences, it ... [more ▼]

The bovine cDNA encoding CD11 a cell-surface glycoprotein involved in multiple leukocyte functions, was sequenced and compared with the human and murine sequences. Despite some focal differences, it shares all the main characteristics of its known mammalian homologs. Along with the bovine CD18-encoding cDNA, which is available for a long time, the sequence data provided here will allow the successful expression of bovine CD11a, thus giving the first opportunity to express the Bos taurus beta(2)-integrin CD11a/CD18 (LFA-1, alpha(L)beta(2)) in vitro as a tool to examine the specificities of inflammation in the bovine species. (C) 2003 Elsevier B.V. All rights reserved. [less ▲]

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See detailStructural Similarities and Evolutionary Relationships in Chloride-Dependent Alpha-Amylases
D'Amico, Salvino ULiege; Gerday, Charles ULiege; Feller, Georges ULiege

in Gene (2000), 253(1), 95-105

The alpha-amylase sequences contained in databanks were screened for the presence of amino acid residues Arg195, Asn298 and Arg/Lys337 forming the chloride-binding site of several specialized alpha ... [more ▼]

The alpha-amylase sequences contained in databanks were screened for the presence of amino acid residues Arg195, Asn298 and Arg/Lys337 forming the chloride-binding site of several specialized alpha-amylases allosterically activated by this anion. This search provides 38 alpha-amylases potentially binding a chloride ion. All belong to animals, including mammals, birds, insects, acari, nematodes, molluscs, crustaceans and are also found in three extremophilic Gram-negative bacteria. An evolutionary distance tree based on complete amino acid sequences was constructed, revealing four distinct clusters of species. On the basis of multiple sequence alignment and homology modeling, invariable structural elements were defined, corresponding to the active site, the substrate binding site, the accessory binding sites, the Ca(2+) and Cl(-) binding sites, a protease-like catalytic triad and disulfide bonds. The sequence variations within functional elements allowed engineering strategies to be proposed, aimed at identifying and modifying the specificity, activity and stability of chloride-dependent alpha-amylases. [less ▲]

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See detailMass-murder deletion of 19 Orfs from Saccharomyces cerevisiae chromosome XI
Vandenbol, Micheline ULiege; Fairhead, C.

in Gene (2000), 247(1-2), 45-52

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See detailThe gene encoding bovine pregnancy-associated glycoprotein-1, an inactive member of the aspartic proteinase family
Xie, S.; Green, J.; Beckers, Jean-François ULiege et al

in Gene (1995), 159(2), 193-197

Bovine pregnancy-associated glycoprotein 1 (bPAG1) is a member of the aspartic proteinase family. It becomes detectable in maternal serum soon after implantation and is produced specifically in the ... [more ▼]

Bovine pregnancy-associated glycoprotein 1 (bPAG1) is a member of the aspartic proteinase family. It becomes detectable in maternal serum soon after implantation and is produced specifically in the invasive binucleate cells of the placenta. As a result of a key mutation within its catalytic center, bPAG1 appears to be proteolytically inactive. Its gene consists of nine exons (size range 99-281 bp) and eight introns (87-1800 bp) organized in a manner very similar to those of proteolytically active mammalian aspartic proteinases. The transcription start point (tsp) is located 53 or 54 bp upstream from the start codon (ATG) and 19 bp downstream from a 5'-TATATAA sequence. Southern blot analyses have indicated the presence of two bPAG1 genes. By screening with an antiserum raised against bPAG1, a less common cDNA with 91% sequence identity to the bPAG1 transcript has been isolated from a placental cDNA library and presumably represents the second gene. At least eight other genes with sequences that hybridize relatively weakly to the bPAG1 probe are present in the bovine genome. Despite the similarities in the transcribed portion of the genes encoding PAG1, pepsinogen and other mammalian aspartic proteinases, the sequences upstream from the tsp of bPAG1 are unique. [less ▲]

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See detailSequence of the triosephosphate isomerase-encoding gene isolated from the thermophile Bacillus stearothermophilus
Rentier-Delrue, Françoise ULiege; Moyens, Sylvianne; Lion, Michelle ULiege et al

in Gene (1993), 134(1), 137-8

By analysis of genomic clones, we have determined the complete nucleotide sequence of the gene encoding triosephosphate isomerase (TIM; EC 5.3.1.1) in the thermophilic bacterium, Bacillus ... [more ▼]

By analysis of genomic clones, we have determined the complete nucleotide sequence of the gene encoding triosephosphate isomerase (TIM; EC 5.3.1.1) in the thermophilic bacterium, Bacillus stearothermophilus. The gene encodes a 253-amino-acid TIM which is 39% identical to that of the mesophile, Escherichia coli. [less ▲]

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See detailStabilization of T7-Promoter-Based Parhs Expression Vectors Using the Parb Locus
De Moerlooze, L.; Struman, Ingrid ULiege; Renard, Andre et al

in Gene (1992), 119(1), 91-3

We describe a modification of the pAR3040 vector which results in its efficient stabilization during cell division. The parB locus of the plasmid R1 was introduced into the plasmid, pAR3040, to construct ... [more ▼]

We describe a modification of the pAR3040 vector which results in its efficient stabilization during cell division. The parB locus of the plasmid R1 was introduced into the plasmid, pAR3040, to construct the pARHS vectors. These vectors are stable for at least 60 cell generations, even in the absence of selection by an antibiotic present in the culture media, both with or without IPTG induction. [less ▲]

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See detailSequence of the Subtilisin-Encoding Gene from an Antarctic Psychrotroph Bacillus Ta41
Davail, S.; Feller, Georges ULiege; Narinx, E. et al

in Gene (1992), 119(1), 143-4

The nucleotide sequence of the subtilisin-encoding gene from the antarctic psychrotroph, Bacillus TA41, was determined. The primary structure of the subtilisin precursor corresponds to a preproenzyme of ... [more ▼]

The nucleotide sequence of the subtilisin-encoding gene from the antarctic psychrotroph, Bacillus TA41, was determined. The primary structure of the subtilisin precursor corresponds to a preproenzyme of 419 amino acids. Asp144, His181 and Ser359 are the proposed catalytic residues of the protease active site. [less ▲]

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See detailCloning and Expression in Escherichia Coli of Three Lipase-Encoding Genes from the Psychrotrophic Antarctic Strain Moraxella Ta144
Feller, Georges ULiege; Thiry, M.; Arpigny, J. L. et al

in Gene (1991), 102(1), 111-5

The cloning and expression of genes from a psychrotrophic bacterium in a mesophilic host are described. Three lipase (Lip)-encoding genes (lip) from the antarctic psychrotroph, Moraxella TA144, were ... [more ▼]

The cloning and expression of genes from a psychrotrophic bacterium in a mesophilic host are described. Three lipase (Lip)-encoding genes (lip) from the antarctic psychrotroph, Moraxella TA144, were cloned by inserting Sau3AI-generated DNA fragments into the BamHI site of the pSP73 plasmid vector. To prevent heat denaturation of the gene product, the screening procedure on agar plates containing an emulsified lipid involved growing of Escherichia coli recombinant colonies at 25 degrees C followed by incubation at 0 degree C. The three recombinant (reLip) were cell-associated and differed by their respective specificity towards p-nitrophenyl esters of various aliphatic chain lengths. These cloned reLip conserved the main character of the wild-type enzymes, i.e. a dramatic shift of the optimal temperature of activity towards low temperatures and pronounced heat lability. [less ▲]

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See detailExpression in Escherichia coli of two mutated genes encoding the cholera toxin B subunit
L'Hoir, C.; Renard, A.; Martial, Joseph ULiege

in Gene (1990), 89(1), 47-52

To allow subsequent genetically mediated fusion of foreign antigens to cholera toxin B subunit (CTB), two mutated CTB encoding genes (ctxB) were constructed and overexpressed in Escherichia coli. The ... [more ▼]

To allow subsequent genetically mediated fusion of foreign antigens to cholera toxin B subunit (CTB), two mutated CTB encoding genes (ctxB) were constructed and overexpressed in Escherichia coli. The signal peptide coding sequence was deleted and restriction sites were created at both ends of the modified sequence. Both synthesized CTBs contain additional amino acid(s) at the N terminus (one and three). They were purified as insoluble products and refolded into the natural pentameric CTB structure by a denaturation-renaturation cycle. After renaturation, both recombinant proteins recovered CTB antigenicity and the ability to bind to GM1 gangliosides, as shown by in vitro analysis. Preliminary data indicated that both properties were unaltered by fusion of a foreign peptide to the mutated CTBs. [less ▲]

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