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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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Sequences of Human GLTP Genes and Predicted Translation Products. A. Nucleotide ORF Sequences of 5-exon/4-intron GLTP and intronless GLTP (GLTPi). The black horizontal lines show the locations of the GLTP 'universal primers' used for PCR analyses. B. Encoded Amino Acid Sequences of Human GLTP Homologs. Different sequence coloring distinguishes the exon source of 5-exon/4-intron GLTP.
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Figure 2: Sequences of Human GLTP Genes and Predicted Translation Products. A. Nucleotide ORF Sequences of 5-exon/4-intron GLTP and intronless GLTP (GLTPi). The black horizontal lines show the locations of the GLTP 'universal primers' used for PCR analyses. B. Encoded Amino Acid Sequences of Human GLTP Homologs. Different sequence coloring distinguishes the exon source of 5-exon/4-intron GLTP.

Mentions: Alignment of the human cDNA ORFs (630 bases) encoding GLTP (AF209074, AY372530, AY372531, AY372532) also revealed ~94% homology with a single genomic DNA sequence at locus 11p15.1 in chromosome 11 (Figure 2A). The genomic sequence (627 bases) contained both start (ATG) and stop (TAA) codons and encoded a near full-length GLTP-like protein (208 a.a.) lacking only Lys146 (Figure 2A). Absent from the GLTP-like sequence was AGA from within the CAG435AAGATC TTC444 region, affecting two potential codons (Figure 2A; cyan highlight). Fortuitously, the deleterious effect of the missing AGA was minimized and resulted only in the loss of a single lysine residue. The remaining CAG435ATC TTC441 sequence kept the reading frame fidelity in tact without alteration of subsequent codons. Altogether, nucleotide deletions and substitutions delineated a total of 13 different amino acids in the GLTP paralog, resulting in 94% identity with GLTP encoded at locus 12q24.11 (Figure 2B).


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)

Sequences of Human GLTP Genes and Predicted Translation Products. A. Nucleotide ORF Sequences of 5-exon/4-intron GLTP and intronless GLTP (GLTPi). The black horizontal lines show the locations of the GLTP 'universal primers' used for PCR analyses. B. Encoded Amino Acid Sequences of Human GLTP Homologs. Different sequence coloring distinguishes the exon source of 5-exon/4-intron GLTP.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Sequences of Human GLTP Genes and Predicted Translation Products. A. Nucleotide ORF Sequences of 5-exon/4-intron GLTP and intronless GLTP (GLTPi). The black horizontal lines show the locations of the GLTP 'universal primers' used for PCR analyses. B. Encoded Amino Acid Sequences of Human GLTP Homologs. Different sequence coloring distinguishes the exon source of 5-exon/4-intron GLTP.
Mentions: Alignment of the human cDNA ORFs (630 bases) encoding GLTP (AF209074, AY372530, AY372531, AY372532) also revealed ~94% homology with a single genomic DNA sequence at locus 11p15.1 in chromosome 11 (Figure 2A). The genomic sequence (627 bases) contained both start (ATG) and stop (TAA) codons and encoded a near full-length GLTP-like protein (208 a.a.) lacking only Lys146 (Figure 2A). Absent from the GLTP-like sequence was AGA from within the CAG435AAGATC TTC444 region, affecting two potential codons (Figure 2A; cyan highlight). Fortuitously, the deleterious effect of the missing AGA was minimized and resulted only in the loss of a single lysine residue. The remaining CAG435ATC TTC441 sequence kept the reading frame fidelity in tact without alteration of subsequent codons. Altogether, nucleotide deletions and substitutions delineated a total of 13 different amino acids in the GLTP paralog, resulting in 94% identity with GLTP encoded at locus 12q24.11 (Figure 2B).

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