Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

Abstract

Phosphoketolases (XFPs) are glycolytic enzymes present in several organisms belonging to the Eukarya and Bacteria domains. A total of 151 putative xfp genes were detected in 650 complete genomes available in public databases. Elimination of redundant sequences and pseudogenes rendered a final data set of 128 phosphoketolases, which was analyzed by phylogenetic methods. The distribution of xfp genes was uneven in most taxonomic groups, with the exception of the taxonomical division Lactobacillaceae, in which all the species studied harbored a putative xfp gene. Putative xfp genes were also present predominantly in Rhizobiales and Actinobacteria divisions, in which 23 out of 28 genomes and 23 out of 41 genomes contained at least one putative xfp homolog, respectively. Phylogenetic analyses showed clear discordance with the expected order of organismal descent even in groups where xfp is prevalent, such as Lactobacillaceae. The presence of putative paralogs in some organisms cannot account for these discrepancies; instead, these paralogs are most possibly xenologs. The results of the phylogenetic analyses, the distribution of xfp genes and the location of some xfp genes in plasmids are independent pieces of evidence that point to horizontal gene transfer as a major driving force in the evolution of phosphoketolases.

Catabolism of Glucose and Lactose in Bifidobacterium animalis subsp. lactis, Studied by 13 C Nuclear Magnetic Resonance

“…As expected, the profile of [1-13 C Gal ]Lac consumption fully resembled that of [1][2][3][4][5][6][7][8][9][10][11][12][13] C Glc ]Lac consumption, displaying biphasic kinetics and similar values for the maximal rate of utilization ( Fig. 4; compare Fig.…”

“…Moreover, we used perchloric acid cell extract experiments to confirm that Glc and Lac metabolism in BB-12 goes through by the bifid shunt. For this purpose, we characterized the metabolism of [1-13 C]Glc, [2][3][4][5][6][7][8][9][10][11][12][13] C]Glc, and [3-13 C]Glc in Glc-grown cells and we used [1][2][3][4][5][6][7][8][9][10][11][12][13] C Glc ]Lac, [1- 13 C Gal ]Lac, and [1-13 C]Glc in Lac-grown cells to unravel the partitioning of sugar substrate carbon throughout the metabolic network of this strain. Abbreviations: ␤-Gal, ␤-galactosidase; Pgm, phosphoglucomutase; GlkA, glucokinase; Gpi, Glc 6-phosphate isomerase; Xfp, fructose 6-phosphate phosphoketolase; Adh2, alcohol dehydrogenas; AckA, acetate kinase; Ldh2, lactate dehydrogenase; Pfl, pyruvate formate lyase; Tal, transaldolase; Tkt, transketolase; GalK, galactokinase; GalT, galactose 1-phosphate uridylyltransferase; UgpA, UTP-Glc 1-phosphate uridylyltransferase; GalE, UDP-Glc 4-epimerase; Gap, glyceraldehyde 3-phosphate dehydrogenase; Pgk, phosphoglycerate kinase; Gpm, phosphoglycerate mutase; Eno, enolase, Pyk, pyruvate kinase; Glc, glucose; Gal, galactose; Gal1P, galactose 1-phosphate; Glc1P, glucose 1-phosphate; Glc6P, glucose 6-phosphate; F6P, fructose 6-phosphate; E4P, erythrose 4-phosphate; S7P, sedoheptulose 7-phosphate; R5P, ribulose 5-phopshate; X5P, xylulose 5-phosphate; GAP, glyceraldehyde 3-phosphate; 1,3-BPG, 1,3-bisphopshoglycerate; 3-PGA, 3-phosphoglycerate; 2-PGA, 2-phosphoglycerate; PEP, phosphoenolpyruvate; Lactate Out , extracellular lactate; Acetate out , extracellular acetate.…”

Role of Extracellular Transaldolase from Bifidobacterium bifidum in Mucin Adhesion and Aggregation

“…The protein was identified by mass spectrometry analysis as transaldolase (Tal, BBPR_1029) (46). This enzyme is involved in the pentose phosphate pathway and is responsible for the conversion of fructose-6-P and erythrose-4-P into sedoheptulose-7-P and glyceraldehyde-3-P, the latter entering directly into the glycolytic pathway (43). Although its cytoplasmic location is generally agreed, some clues point to the fact that in several Bifidobacterium species it could be released in the extracellular milieu.…”

Crystal Structures of Phosphoketolase

“…These enzymes constitute two homologous (sequence identity Ͼ 40%) but phylogenetically distinct groups (supplemental Figs. 1 and 2 and supplemental Table 1) (17). PKs catalyze the cleavage of X5P or F6P (donor) utilizing P i as the acceptor (phosphorolysis) to produce acetyl-P, water, and glyceraldehyde 3-phosphate or erythrose 4-phosphate.…”

“…XPK is a key enzyme in the pentose catabolism in various microbes, including filamentous fungi and yeasts (17). This pentose catabolism is called the "PK pathway" (20).…”