Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism
Ron S. Ronimus (1, 2) and Hugh W. Morgan (1)
1. Thermophile Research Unit, Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand / 2. Author to whom correspondence should be addressed ([email protected]) / Received June 17, 2002; accepted October 24, 2002; published online November 28, 2002
Enzymes of the gluconeogenic/glycolytic pathway (the Embden-Meyerhof-Parnas (EMP) pathway), the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle and the Entner-Doudoroff pathway are widely distributed and are often considered to be central to the origins of metabolism. In particular, several enzymes of the lower portion of the EMP pathway (the so-called trunk pathway), including triosephosphate isomerase (TPI; EC 220.127.116.11), glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 18.104.22.168/13), phosphoglycerate kinase (PGK; EC 22.214.171.124) and enolase (EC 126.96.36.199), are extremely well conserved and universally distributed among the three domains of life. In this paper, the distribution of enzymes of gluconeogenesis/glycolysis in hyperthermophiles—microorganisms that many believe represent the least evolved organisms on the planet—is reviewed. In addition, the phylogenies of the trunk pathway enzymes (TPIs, GAPDHs, PGKs and enolases) are examined. The enzymes catalyzing each of the six-carbon transformations in the upper portion of the EMP pathway, with the possible exception of aldolase, are all derived from multiple gene sequence families. In contrast, single sequence families can account for the archaeal and hyperthermophilic bacterial enzyme activities of the lower portion of the EMP pathway. The universal distribution of the trunk pathway enzymes, in combination with their phylogenies, supports the notion that the EMP pathway evolved in the direction of gluconeogenesis, i.e., from the bottom up.
Keywords: enolase, evolution, gluconeogenesis, glyceraldehyde-3-phosphate dehydrogenase, glycolysis, origins of life, phosphoglycerate kinase, triosephosphate isomerase.