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Human glycolipid transfer protein (GLTP) genes: organization, transcriptional status and evolution.

Zou X, Chung T, Lin X, Malakhova ML, Pike HM, Brown RE - BMC Genomics (2008)

Bottom Line: In human cells, single-copy GLTP genes were found in chromosomes 11 and 12.Active transcription was found for 12q24.11 GLTP but 11p15.1 GLTP was transcriptionally silent.A solid foundation has been established for future identification of hereditary defects in human GLTP genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA. xzou@hi.umn.edu

ABSTRACT

Background: Glycolipid transfer protein is the prototypical and founding member of the new GLTP superfamily distinguished by a novel conformational fold and glycolipid binding motif. The present investigation provides the first insights into the organization, transcriptional status, phylogenetic/evolutionary relationships of GLTP genes.

Results: In human cells, single-copy GLTP genes were found in chromosomes 11 and 12. The gene at locus 11p15.1 exhibited several features of a potentially active retrogene, including a highly homologous (approximately 94%), full-length coding sequence containing all key amino acid residues involved in glycolipid liganding. To establish the transcriptional activity of each human GLTP gene, in silico EST evaluations, RT-PCR amplifications of GLTP transcript(s), and methylation analyses of regulator CpG islands were performed using various human cells. Active transcription was found for 12q24.11 GLTP but 11p15.1 GLTP was transcriptionally silent. Heterologous expression and purification of the GLTP paralogs showed glycolipid intermembrane transfer activity only for 12q24.11 GLTP. Phylogenetic/evolutionary analyses indicated that the 5-exon/4-intron organizational pattern and encoded sequence of 12q24.11 GLTP were highly conserved in therian mammals and other vertebrates. Orthologs of the intronless GLTP gene were observed in primates but not in rodentiates, carnivorates, cetartiodactylates, or didelphimorphiates, consistent with recent evolutionary development.

Conclusion: The results identify and characterize the gene responsible for GLTP expression in humans and provide the first evidence for the existence of a GLTP pseudogene, while demonstrating the rigorous approach needed to unequivocally distinguish transcriptionally-active retrogenes from silent pseudogenes. The results also rectify errors in the Ensembl database regarding the organizational structure of the actively transcribed GLTP gene in Pan troglodytes and establish the intronless GLTP as a primate-specific, processed pseudogene marker. A solid foundation has been established for future identification of hereditary defects in human GLTP genes.

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Phylogenetic Tree of 5-exon/4-intron GLTP Gene. Numbers correspond to percentages of bootstrap support for each node from the maximum parsimony, distance, and minimum evolution analyses. (Nucleotide and amino acid sequence alignments are provided as Additional file 1, Figures S4 and S5).
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Figure 6: Phylogenetic Tree of 5-exon/4-intron GLTP Gene. Numbers correspond to percentages of bootstrap support for each node from the maximum parsimony, distance, and minimum evolution analyses. (Nucleotide and amino acid sequence alignments are provided as Additional file 1, Figures S4 and S5).

Mentions: Phylogenetic analyses (Figure 6) indicated that all sequences produced exactly the same tree topology by three independent methods [neighbor-joining (NJ), maximum parsimony (MP) and minimum evolution (ME)] [39,40]. Most of the major internal branches were well supported (Figure 6). Overall, the phylogenetic/evolutionary relationships observed for the 5-exon/4-intron GLTP gene conformed to the widely-accepted phylogeny of vertebrates. The situation for GLTPi was much different. Orthologs of the human GLTPi gene were discovered only in nonhuman primates (chimpanzee, macaque) and were not present in carnivora (dog), cetartiodactyla (pig, cow), rodentia (mouse, rat) or didelphimorphia (opossum), suggesting recent evolutionary development. The 'intronless' nature of the ORF sequences was consistent with origination by retrotransposition of mRNA derived from an ancestral 5-exon/4-intron GLTP gene. The structural features supporting the common evolutionary ancestry of GLTPi genes in primates, included the following differences compared to their 5-exon/4-intron GLTP genes: 1) location on a different chromosome; 2) occurrence of nearly full-length GLTP ORFs (624 bases) including both start and stop codons; 3) absence of AGA at the same location in the sequence; 4) presence of the CAG435ATC TTC441 sequence (after AGA deletion from the CAG435AAGATC TTC444 region), keeping the potential reading frame fidelity intact and limiting downstream changes. The locations of the base changes within the affected GLTPi sequences are shown in Additional file 1, Figure S3. These shared and delineating features provided an unequivocal indication of the close evolutionary relationship among the GLTPi genes of primates.


Human glycolipid transfer protein (GLTP) genes: organization, transcriptional status and evolution.

Zou X, Chung T, Lin X, Malakhova ML, Pike HM, Brown RE - BMC Genomics (2008)

Phylogenetic Tree of 5-exon/4-intron GLTP Gene. Numbers correspond to percentages of bootstrap support for each node from the maximum parsimony, distance, and minimum evolution analyses. (Nucleotide and amino acid sequence alignments are provided as Additional file 1, Figures S4 and S5).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2262070&req=5

Figure 6: Phylogenetic Tree of 5-exon/4-intron GLTP Gene. Numbers correspond to percentages of bootstrap support for each node from the maximum parsimony, distance, and minimum evolution analyses. (Nucleotide and amino acid sequence alignments are provided as Additional file 1, Figures S4 and S5).
Mentions: Phylogenetic analyses (Figure 6) indicated that all sequences produced exactly the same tree topology by three independent methods [neighbor-joining (NJ), maximum parsimony (MP) and minimum evolution (ME)] [39,40]. Most of the major internal branches were well supported (Figure 6). Overall, the phylogenetic/evolutionary relationships observed for the 5-exon/4-intron GLTP gene conformed to the widely-accepted phylogeny of vertebrates. The situation for GLTPi was much different. Orthologs of the human GLTPi gene were discovered only in nonhuman primates (chimpanzee, macaque) and were not present in carnivora (dog), cetartiodactyla (pig, cow), rodentia (mouse, rat) or didelphimorphia (opossum), suggesting recent evolutionary development. The 'intronless' nature of the ORF sequences was consistent with origination by retrotransposition of mRNA derived from an ancestral 5-exon/4-intron GLTP gene. The structural features supporting the common evolutionary ancestry of GLTPi genes in primates, included the following differences compared to their 5-exon/4-intron GLTP genes: 1) location on a different chromosome; 2) occurrence of nearly full-length GLTP ORFs (624 bases) including both start and stop codons; 3) absence of AGA at the same location in the sequence; 4) presence of the CAG435ATC TTC441 sequence (after AGA deletion from the CAG435AAGATC TTC444 region), keeping the potential reading frame fidelity intact and limiting downstream changes. The locations of the base changes within the affected GLTPi sequences are shown in Additional file 1, Figure S3. These shared and delineating features provided an unequivocal indication of the close evolutionary relationship among the GLTPi genes of primates.

Bottom Line: In human cells, single-copy GLTP genes were found in chromosomes 11 and 12.Active transcription was found for 12q24.11 GLTP but 11p15.1 GLTP was transcriptionally silent.A solid foundation has been established for future identification of hereditary defects in human GLTP genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA. xzou@hi.umn.edu

ABSTRACT

Background: Glycolipid transfer protein is the prototypical and founding member of the new GLTP superfamily distinguished by a novel conformational fold and glycolipid binding motif. The present investigation provides the first insights into the organization, transcriptional status, phylogenetic/evolutionary relationships of GLTP genes.

Results: In human cells, single-copy GLTP genes were found in chromosomes 11 and 12. The gene at locus 11p15.1 exhibited several features of a potentially active retrogene, including a highly homologous (approximately 94%), full-length coding sequence containing all key amino acid residues involved in glycolipid liganding. To establish the transcriptional activity of each human GLTP gene, in silico EST evaluations, RT-PCR amplifications of GLTP transcript(s), and methylation analyses of regulator CpG islands were performed using various human cells. Active transcription was found for 12q24.11 GLTP but 11p15.1 GLTP was transcriptionally silent. Heterologous expression and purification of the GLTP paralogs showed glycolipid intermembrane transfer activity only for 12q24.11 GLTP. Phylogenetic/evolutionary analyses indicated that the 5-exon/4-intron organizational pattern and encoded sequence of 12q24.11 GLTP were highly conserved in therian mammals and other vertebrates. Orthologs of the intronless GLTP gene were observed in primates but not in rodentiates, carnivorates, cetartiodactylates, or didelphimorphiates, consistent with recent evolutionary development.

Conclusion: The results identify and characterize the gene responsible for GLTP expression in humans and provide the first evidence for the existence of a GLTP pseudogene, while demonstrating the rigorous approach needed to unequivocally distinguish transcriptionally-active retrogenes from silent pseudogenes. The results also rectify errors in the Ensembl database regarding the organizational structure of the actively transcribed GLTP gene in Pan troglodytes and establish the intronless GLTP as a primate-specific, processed pseudogene marker. A solid foundation has been established for future identification of hereditary defects in human GLTP genes.

Show MeSH