Presence of Prokaryotic and Eukaryotic Species in All Subgroups of the PP _i -Dependent Group II Phosphofructokinase Protein Family

Abstract

Inorganic pyrophosphate-dependent phosphofructokinase (PP i -PFK) of the amitochondriate eukaryote Mastigamoeba balamuthi was sequenced and showed about 60% identity to PP i -PFKs from two eubacteria, Propionibacterium freudenreichii and Sinorhizobium meliloti. These gene products represent a newly recognized lineage of PFKs. All four lineages of group II PFKs, as defined by phylogenetic analysis, contained both prokaryotic and eukaryotic species, underlining the complex evolutionary history of this enzyme.We have recently extended our studies on glycolytic enzymes of parasitic amitochondriate eukaryotes (20) to the free-living Mastigamoeba balamuthi (ATCC 30984) (6) with the goal of comparing the metabolic properties of anaerobic and microaerophilic eukaryotes with dramatically different life styles. This species belongs to the pelobionts, a group of amitochondriate amoeboflagellate protists of uncertain evolutionary position (5, 25). We noted that the sequence of its phosphofructokinase (PFK) showed unexpected characteristics, prompting us to revisit the taxonomic distribution and relationships of various PFK types.Type A PFK, an enzyme of the glycolytic pathway, phosphorylates fructose 6-phosphate to fructose 1,6-bisphosphate. In most organisms, ATP is the phosphoryl donor (ATP-PFK; EC 2.7.1.11) of the irreversible reaction. A number of protists and plants and some eubacteria contain reversible PFKs, which use inorganic pyrophosphate (PP i ) instead of ATP (PP i -PFK; EC 2.7.1.90). The assumed significance of PP i as the phosphoryl donor is reflected in an increase of the ATP yield during glycolysis (16,26). This notion is supported by the predominant occurrence of PP i -PFK in organisms living in hypoxic or anoxic environments, which rely on anaerobic glycolysis (17).The evolutionary history of PFK does not coincide with accepted notions of organismic relationships and points to past gene duplications and lateral gene transfers. Based primarily on sequence characteristics, type A PFKs are currently assigned to three major groups (groups I, II, and III) (22). Group II can be further subdivided into four subgroups, which appear as robust clades in phylogenetic reconstructions (we are using the tentative nomenclature proposed for clades in group II [18]). Closely related organisms may contain close homologs of PFK which use different phosphoryl donors, indicating that enzyme specificity can change relatively easily (2), a conclusion recently confirmed experimentally (7). Some organisms even contain members of two such subgroups (8, 10-12). Phylogenetic analysis. Sequences of PP i -PFK homologs were retrieved from the National Center for Biotechnology Information protein database. The S. meliloti PFK sequence was retrieved from the website of the corresponding genome project (http://sequence.toulouse.inra.fr/meliloti.html) (3). Sequence sampling for group II encompasses the whole diversity present in the nonredundant National Center for Biotechnology Information database. Sampling of group III was restricted to ...

Niche metabolism in parasitic protozoa

“…Even here, however, specialized biochemical twists maximize the ATP yield from what could be considered an inefficient catabolism of fuel sources. For instance, in glycolysis, which provides the major energy generating pathway, the phosphofructokinase from several enteric (intestinal) parasites is pyrophosphate (PP i ) rather than ATP dependent (Denton et al 1996;Muller et al 2001). In Giardia, E. histolytica, and probably Cryptosporidium too, the glycolytic end-product, pyruvate, can be metabolized to acetyl-CoA, which is then the substrate for acetyl-CoA synthetase.…”

Phylogeny vs genome reshuffling: horizontal gene transfer

“…Amino acids essential for ATP-PFK and PPi-phosphofructokinase (PFP) at 104 and 124 position [120]. Several duplication and HGT fl ux the phylogeny of PFK [121]. Conservation Aquifex aeolicus and Thermotoga maritima Large number of genes that are most similar in their protein [117] Archaeoglobus fulgidus Fatty acid metabolism; Tryptophan biosynthesis pathway closely related to eubacterium Bacillus subtilis [73,117] Bacillus subtilis and B. halodurans Prophage like regions [117] Bacteria and fungi ß-glucuronidase (gus) genes [159] Bacteria and archaea FtsZ, a cell division protein [160,161] Bacteria and rumen Ciliates Expressed genes [162] Chlamydia trachomatis Polymorphic membrane protein C gene [163] Clostridium acetobutylicum 3-Isopropylmalate dehydratase, small subunit 3-Isopropylmalate dehydratase, large subunit 2-Isopropylmalate synthase [164] Cyanobacteria and α-proteobacteria (Rickettsia and Ehrlichia) are nearest to chloroplast and mitochondria HSP60, a major bacterial antigenic protein [165,166] Cyanobacteria and γ-proteobacteria ArsC gene (arsenate reductase) [167] Cyanobacteria and chloroplast genome of Euglena myxocylindracea psbA intron [168] Deinococcus radiodurans dTDP-4-dehydrorhamnose epimerase (Lipopolysaccharide biosynthesis) [118,164] …”

Pyruvate-Phosphate Dikinase of Oxymonads and Parabasalia and the Evolution of Pyrophosphate-Dependent Glycolysis in Anaerobic Eukaryotes

“…A cytoplasmic isoenzyme of unclear function also exists in C3 and C4 plants, and it has been suggested that it may have a glycolytic role, especially in oxygen-starved tissues (22). Trypanosomatids target PPDK to glycosomes where it fulfills a thermodynamic role of pyrophosphate recycling in place of pyrophosphatase (1).At present, studies on the molecular evolution of PP i -linked glycolysis have focused almost exclusively on PFK and PFP (3,27). These proteins are homologous, and the gene family has had a complex evolutionary history including multiple events of duplication, loss, and lateral gene transfer (3,27).…”

“…At present, studies on the molecular evolution of PP i -linked glycolysis have focused almost exclusively on PFK and PFP (3,27). These proteins are homologous, and the gene family has had a complex evolutionary history including multiple events of duplication, loss, and lateral gene transfer (3,27).…”

“…These proteins are homologous, and the gene family has had a complex evolutionary history including multiple events of duplication, loss, and lateral gene transfer (3,27). In contrast, the phylogeny of PPDK has not been extensively explored.…”