The Phosphoglycerate Kinase (Pgk) Gene Family - An Example of Evolution by Gene Duplication

We have investigated the phosphoglycerate kinase (Pgk) gene family to test certain predictions of Susumo Ohno’s theory of Evolution by Gene Duplication. Specifically, we have examined multiple genome databases for evidence that the Pgk2 retrogene has accumulated DNA sequence changes subsequent to its origin by retroposition that have facilitated the evolution of certain specialized functions in this gene that are distinct from those in the Pgk1 gene which has retained characteristics and functions similar to the progenitor Pgk gene. The specializations investigated in the Pgk2 gene include potential unique sequences in 1) the promoter region to confer tissue-specific regulation of transcription, 2) the 3’−untranslated region to confer posttranscriptional regulation, and 3) the coding sequence to confer regulation of intracellular localization of the encoded protein. Our bioinformatics analyses using 11 eutherian Pgk genes indicates that at the transcriptional level, the Pgk1 promoters have conserved a CpG−island whereas the Pgk2 genes seem to have lost the CpG−island presumably present after retroposition. The metatherian opossum Pgk1 promoter has conserved a CpG−island. The Pgk2 promoters in opossum, tammar wallaby, and Tasmanian devil (all metatherian species) also contain CpG−islands of varying strengths. In addition, the eutherian Pgk1 core promoters have conserved two CAAT−/GC−box pairs and a single NF1−like element, while the Pgk2 core promoters have conserved a single CAAT−/GC−box pair and gained an E3/E4 enhancer sequence essential for testis−specific expression that appears to have derived from the NF1−like element. The opossum (metatherian) Pgk1 core promoter has conserved a CAAT−box pair and a single GC−box, while surprisingly, the metatherian (opossum and tammar wallaby) Pgk2 core promoters lack CAAT− and GC−boxes, and any other standard core promoter elements. At the posttranscriptional level, our results indicate that seven footprints are conserved in eutherian Pgk1 3’−UTRs, but these are not generally found in eutherian Pgk2 3’−UTRs. Pgk2 3’−UTRs have retained only one element also found in Pgk1 3’−UTRs, but have gained multiple novel elements not present in Pgk1 3’−UTRs, including two putative PTBP2 binding sites important for Pgk2 mRNA stability. In addition, the opossum Pgk1 3’−UTR has conserved three of the seven elements observed in eutherian Pgk1 3’−UTRs, and two of these are also observed in the putative Tasmanian devil Pgk1 3’−UTR. Unlike the promoter sequences regulating testis−specific transcription of the Pgk2 gene and the 3’−UTR sequences regulating posttranscriptional delay of the Pgk2 mRNA, we did not find any specific conserved sequences within the eutherian PGK2 coding region that appear to regulate intracellular localization of the PGK protein. Overall, the eutherian and metatherian comparative studies support the idea that the Pgk2 promoter and 3’−UTR diverged from Pgk1−like sequences by gradually acquiring sequence changes leading to two specialized functions associated with the Pgk2 gene —testis−specific expression and translational delay, both of which facilitate expression of the PGK2 isozyme in eutherian spermatogenic cells. Therefore, our results are consistent with Ohno’s theory of Evolution by Gene Duplication.