3 research outputs found
The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution
BACKGROUND:Giardia lamblia trophozoites colonize the intestines of susceptible mammals and cause diarrhea, which can be prolonged despite an intestinal immune response. The variable expression of the variant-specific surface protein (VSP) genes may contribute to this prolonged infection. Only one is expressed at a time, and switching expression from one gene to another occurs by an epigenetic mechanism.RESULTS:The WB Giardia isolate has been sequenced at 10x coverage and assembled into 306 contigs as large as 870 kb in size. We have used this assembly to evaluate the genomic organization and evolution of the vsp repertoire. We have identified 228 complete and 75 partial vsp gene sequences for an estimated repertoire of 270 to 303, making up about 4% of the genome. The vsp gene diversity includes 30 genes containing tandem repeats, and 14 vsp pairs of identical genes present in either head to head or tail to tail configurations (designated as inverted pairs), where the two genes are separated by 2 to 4 kb of non-coding DNA. Interestingly, over half the total vsp repertoire is present in the form of linear gene arrays that can contain up to 10 vsp gene members. Lastly, evidence for recombination within and across minor clades of vsp genes is provided.CONCLUSIONS:The data we present here is the first comprehensive analysis of the vsp gene family from the Genotype A1 WB isolate with an emphasis on vsp characterization, function, evolution and contributions to pathogenesis of this important pathogen.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]
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Assembly and promoter analysis of variant-specific surface protein (vsp) genes of Giardia lamblia
Giardia lamblia undergoes antigenic variation of variant-specific surface proteins (VSPs) that are encoded by a family of ~150 vsp genes only one of which is expressed at a time. The vsp gene promoters have not been previously studied. A comparison of the upstream non-coding region of vsp genes shows that they lack the AT-rich regions found in other Giardia gene promoters. We have determined that the core promoters of vsp A6 and vsp C5 genes extend from -57 to + 6 and -50 to + 6 respectively. Through linker scanning analysis, we have also identified regions within the vsp A6 core promoter important for promoter activity that span -7-3, -12-8, -17-13 and -42-38.There is no sequence similarity in the upstream regions of the previously characterized vsp genes that were analyzed, with the exception of a seven nucleotide region that encompasses the translation initiation site: Py A A T G T T. We have demonstrated that the four nucleotides flanking the start codon are essential for promoter activity. This result suggests that it may be an Inr element, which by definition determines the site of transcription initiation. In addition, this element loosely resembles the metazoan Inr consensus: Py Py A A/T Py Py. Using 5′ RACE I have determined that for two vsp genes, the translation and transcription start sites are synonymous and reside within this conserved element. However, we were unable to identify protein factors that bind this region using electrophoretic mobility shift assays.A search for characteristic VSP motifs, such as CRGKA, amongst identified ORFs in the Giardia genome assembly in turn identified 180 ORFs which may be VSPs. Eighty one of these are found within contigs while 99 of these are found at contig and 80 ORFs have the Inr element identified in this study.This study supports the hypothesis that longer upstream non-coding regions of vsp genes play a role in regulating the expression of these genes and hence antigenic variation in G. lamblia
The <it>Giardia lamblia vsp </it>gene repertoire: characteristics, genomic organization, and evolution
Abstract Background Giardia lamblia trophozoites colonize the intestines of susceptible mammals and cause diarrhea, which can be prolonged despite an intestinal immune response. The variable expression of the variant-specific surface protein (VSP) genes may contribute to this prolonged infection. Only one is expressed at a time, and switching expression from one gene to another occurs by an epigenetic mechanism. Results The WB Giardia isolate has been sequenced at 10× coverage and assembled into 306 contigs as large as 870 kb in size. We have used this assembly to evaluate the genomic organization and evolution of the vsp repertoire. We have identified 228 complete and 75 partial vsp gene sequences for an estimated repertoire of 270 to 303, making up about 4% of the genome. The vsp gene diversity includes 30 genes containing tandem repeats, and 14 vsp pairs of identical genes present in either head to head or tail to tail configurations (designated as inverted pairs), where the two genes are separated by 2 to 4 kb of non-coding DNA. Interestingly, over half the total vsp repertoire is present in the form of linear gene arrays that can contain up to 10 vsp gene members. Lastly, evidence for recombination within and across minor clades of vsp genes is provided. Conclusions The data we present here is the first comprehensive analysis of the vsp gene family from the Genotype A1 WB isolate with an emphasis on vsp characterization, function, evolution and contributions to pathogenesis of this important pathogen.</p