Suspected Utility of Enzymes with Multiple Activities in the Small GenomeMycoplasmaSpecies: The Replacement of the Missing "Household" Nucleoside Diphosphate Kinase Gene and Activity by Glycolytic Kinases

Abstract

The small genome Mollicutes whose DNAs are completely sequenced (Mycoplasma genitalium, Mycoplasma pneumoniae, Mycoplasma pulmonis, and Ureaplasma urealyticum [parvum]) lack a gene (ndk) for the presumably essential nucleoside diphosphate kinase (NDPK). We hypothesized that other activities might replace NDPK activity. We found in M. genitalium G37(T), Mycoplasma pneumoniae FH(T), Mycoplasma fermentans PG18(T), and Mycoplasma capricolum subsp. capricolum Kid(T) that their 6-phosphofructokinases (6-PFKs), phosphoglycerate kinases (PGKs), pyruvate kinases (PKs), and acetate kinases (AKs), besides reactant ADP/ATP, could use other ribo- and deoxyribo-purine and pyrimidine NDPs and NTPs. These activities could compensate for the absence of an orthologous ndk gene in the Mycoplasmataceae. They suggest a metabolically varied and consequential role for unrelated and perhaps unsuspected "replacement" or compensatory enzymes that may confound metabolic prediction. We partially purified and biochemically characterized the PKs, 6-PFKs, PGKs, and AKs from M. capricolum subsp. capricolum Kid(T) and M. fermentans PG18(T).

Essential genes of a minimal bacterium

“…The loss of functions in these mutants could have been compensated for by other M. genitalium dehydrogenases or reductases. This could be another case of mycoplasma enzymes having a relaxed substrate specificity, as has been reported for lactate͞ malate dehydrogenase (18) and nucleotide kinases (19).…”

“…Although we disrupted both of these three gene cassettes, cells presumably need at least one phosphate transporter, so we added three ABC transporter genes for phosphate importation to our proposed minimal gene set. Relaxed substrate specificity is a recurring theme proposed and shown for several M. genitalium enzymes as a mechanism by which this bacterium meets its metabolic needs with fewer genes (18,19).…”

Mycoplasma penetrans Is Capable of Activating Vγ9/Vδ2 T Cells While Other Human Pathogenic Mycoplasmas Fail To Do So

“…However, both M. gallisepticum and M. penetrans contain the sequence information for most enzymes of the MEP pathway in their genome (Table 2); this finding could be corroborated by a PCR analysis with primers specific for the gcpE gene encoding HMB-PP synthase (GcpE) ( Table 1). Yet, we were not able to identify the kinase YchB in either genome and neither the YgbP protein and HMB-PP reductase (LytB) in M. gallisepticum, suggesting that the function of those enzymes may be complemented by the action of compensatory proteins, as suspected recently with respect to other mycoplasma "household" genes (9).…”

Genome Reduction Promotes Increase in Protein Functional Complexity in Bacteria

“…The loss of a gene might disable a pathway, thereby removing constraints on (and expediting the loss of) other genes in the inactivated pathway (Dagan et al 2006). Alternatively, the function of the lost genes might be complemented by others that can serve as compensatory alternatives (Pollack et al 2002;Catrein and Herrmann 2011;Wagner et al 2011). That the TCA cycle remains functional in M. tuberculosis despite the absence of KDH enzyme implies that another protein, which in this case is the multifunctional a-ketoglutarate decarboxylase (KGD), has taken on this compensatory role (Tian et al 2005;Wagner et al 2011).…”