Bioinformatic studies of vertebrate enolases: multifunctional genes and proteins

Abstract

Enolase (ENO) genes and proteins (ENO; EC 4.2.1.11) serve multiple functions in the body, including catalyzing 2-phospho-d-glycerate hydro-lyase activity in glycolysis, assisting hypoxia tolerance, tumor suppression, plasminogen and DNA binding, and acting as a lens crystallin. Comparative ENO amino acid sequences and structures and ENO gene locations were examined using data from several vertebrate genome projects. Vertebrate ENO1, ENO2, and ENO3 genes usually contained 11 coding exons, while ENO4 (encoding an ENO-like protein, ENOLL) usually contained 14 coding exons. Vertebrate ENOF1 (or ENO5) genes encode an antisense RNA, which may regulate mitochondrial thymidylate synthase activity that contained 12-15 coding exons. Vertebrate ENO1, ENO2, and ENO3 sequences shared 78%-98% identities but only 19%-24% with ENO4 and >10% predicted sequence identities with vertebrate ENOF1. Sequence alignments, key amino acid residues, and conserved predicted secondary and tertiary structures were examined, including active site residues (absent in ENO4 and ENOF1) and sites for Mg2+ and plasminogen binding and for acetylation and phosphorylation. The predicted ENO4 structure contained three N-terminal a-helices, two ߭sheets, a poly-proline segment, and an extended C-terminal sequence in addition to the typical a/ߠbarrel structure reported for ENO1-3 sequences. Potential transcription factor binding sites (TFBS) and CpG islands for regulating ENO gene expression were identified. Human ENO1, ENO2, ENO3, and ENOF1 genes each contained CpG islands in the gene promoter regions consistent with higher-than-average levels of expression. Human ENO3 and ENO1 gene promoters also contained a diverse range of TFBS. The ENO4 gene promoter comprised a CpG island and several TFBS, including AHR1 in the 5'-UTR region, which may suggest a role for ENO4 in aryl hydrocarbon ligand binding or metabolism. Phylogeny studies of vertebrate ENO1, ENO2, and ENO3 genes and enzymes suggested that they originated in a vertebrate ancestor from gene duplication events of an ancestral ENO1-like gene >500 million years ago.