Purine and pyrimidine nucleotide metabolism in Mollicutes

Abstract

Several mollicute genome projects are underway, offering unique opportunities to study genes and metabolic pathways on a genome-wide scale. Here, we have analyzed the conservation and diversity of purine and pyrimidine metabolism in mycoplasmas. An evaluation of discrepancies between genomic analysis and enzymatic data revealed interesting aspects about these organisms. We found important examples in which enzyme activity was reported without the annotation of a corresponding gene. An interesting example concerns phosphopentomutase. In Mollicutes, we have identified CDSs orthologous to sequences recently identified as new phosphopentomutases in archaeobacteria that are structurally related to phosphomannomutases. It is suggested that these sequences could replace the function of phosphopentomutases in mollicutes lacking the canonical phosphopentomutase gene (deoB). Also, the activity of 5'-nucleotidase was reported in mollicutes that do not possess any CDS related to ushA. Hypothetical proteins exhibiting domains similar to newly characterized 5' nucleotidases in Escherichia coli are proposed as possible CDSs related to this enzymatic activity in Mollicutes. Based on our analysis, the reductive genome evolution of Mollicutes does not appear to result in a minimum set of genes nor a minimum set of metabolic functions shared by all mollicute species.

Phytoplasma Genomes: Evolution Through Mutually Complementary Mechanisms, Gene Loss and Horizontal Acquisition

“…The gene encoding Udk is present in the genomes of OYM and AYWB but is missing in PAus and PMali. As in the case of other mollicutes (Bizarro and Schuck 2007), phytoplasmas lack a gene set essential for de novo synthesis of pyrimidine bases. As outlined by Kube et al (2012), phytoplasmas may use imported uridine and cytidine as the entry point for the synthesis of UTP/dTTP and CTP/ dCTP, respectively, building blocks for DNA and RNA.…”

3′-(1,2,3-Triazol-1-yl)-3′-deoxythymidine analogs as substrates for human and Ureaplasma parvum thymidine kinase for structure–activity investigations

“…3,5 Not all organisms have the de novo pathway and the mycoplasma Ureaplasma parvum (Up), previously called Ureaplasma urealyticum, is an example of an organism lacking this pathway and therefore relies entirely on the salvage pathway. [10][11][12] Up is a free-living self-replicating bacteria containing one of the smallest genomes known to date. 10,[12][13][14] and is found in up to 80% of all adults.…”

“…[10][11][12] Up is a free-living self-replicating bacteria containing one of the smallest genomes known to date. 10,[12][13][14] and is found in up to 80% of all adults. [12][13][14] Up colonizes the urogenital tract and has the ability to harvest ATP from urea.…”

“…10,[12][13][14] and is found in up to 80% of all adults. [12][13][14] Up colonizes the urogenital tract and has the ability to harvest ATP from urea. 10,13,14 Up is associated with pregnancy complications such as infertility, altered sperm motility and pneumonia in the neonate.…”

Mycoplasma genitalium: a brief review

“…26 To characterise its genome, M. genitalium falls under the so-called 'low G+C' mycoplasmas because its DNA genome typically has fewer guanine (G) and cytosine (C) DNA bases than adenine (A) and thymine (T), as compared to other bacteria. 27,28 The G+C content in the DNA of most mycoplasmas ranges from 24% to 33%, with M. genitalium at 32%. 4 The significance of the low G+C content is that M. genitalium would have a lower melting temperature (T m ) during the doublestranded DNA denaturation stage of polymerase chain reaction (PCR) assays.…”