Functional genomic studies of dihydroxyacetone utilization in Escherichia coli

Paulsen, Ian T.; Reizer, Jonathan; Jin, Ruzhong; Lin, E. C. C.; Saier, Milton H.

doi:10.1099/00221287-146-10-2343

Cited by 25 publications

(22 citation statements)

References 6 publications

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“…9). EIIA-HPr-EI Dha was purified and shown to be phosphorylated by [ 32 P]PEP in the presence of both EI and HPr but was also shown to be slightly phosphorylated in the presence of EI only (304,640). This is consistent with the absolute requirement for EI in dihydroxyacetone phosphorylation that was determined previously (376).…”

Section: Pep-dependent Dihydroxyacetone Phosphorylationsupporting

confidence: 71%

“…For E. coli, it was observed that the dha operon was induc- ible; i.e., PEP-requiring dihydroxyacetone phosphorylation activity increased when cells were grown on dihydroxyacetone (376,640). It appeared that dha operon induction is mediated by the dephosphorylation of the phosphotransfer proteins, as the inactivation of ptsI or dhaM as well as the replacement of any one of the three phosphorylatable histidyl residues in EIIA-HPr-EI Dha led to the constitutive expression of the dhaKLM operon (37).…”

Section: Pep-dependent Dihydroxyacetone Phosphorylationmentioning

confidence: 99%

“…Distinct DhaK and DhaL proteins are present in bacteria that phosphorylate dihydroxyacetone in a PEP-dependent reaction, whereas in bacteria that use ATP for dihydroxyacetone phosphorylation, such as Citrobacter freundii, DhaK and DhaL are fused to a single protein (153,811). The third cistron encodes a tripartite PTS fusion protein, which was designated DhaH by Paulsen et al (640) and DhaM by Gutknecht et al (304). The corresponding gene is referred to as dhaM (ycgC) or ptsD.…”

Section: Pep-dependent Dihydroxyacetone Phosphorylationmentioning

confidence: 99%

“…Mutations in ptsI or the dha operon abolish phosphorylation of dihydroxyacetone and thereby growth on this carbon source. The E. coli dha operon comprises three cistrons (304,640). dhaK (ycgT) and dhaL (ycgS) encode the dihydroxyacetone kinase subunits DhaK and DhaL (also called DhaK1 and DhaK2, respectively).…”

Section: Pep-dependent Dihydroxyacetone Phosphorylationmentioning

confidence: 99%

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How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria

Deutscher

Francke

Postma

2006

Microbiol Mol Biol Rev

1,187

769

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SUMMARY The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.

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Section: Pep-dependent Dihydroxyacetone Phosphorylationsupporting

confidence: 71%

Section: Pep-dependent Dihydroxyacetone Phosphorylationmentioning

confidence: 99%

Section: Pep-dependent Dihydroxyacetone Phosphorylationmentioning

confidence: 99%

Section: Pep-dependent Dihydroxyacetone Phosphorylationmentioning

confidence: 99%

See 2 more Smart Citations

How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria

Deutscher

Francke

Postma

2006

Microbiol Mol Biol Rev

1,187

769

View full text Add to dashboard Cite

show abstract

“…Instead, it appears that the PTS protein content in a bacterium correlates best with the mode of carbohydrate metabolism utilized by that organism. Bacteria that rely on anaerobic sugar metabolism via glycolysis for energy production generally have the most PTS permeases, as discussed previously (56,57). Thus, almost all bacteria that possess the PTS either are capable of anaerobic sugar utilization via glycolysis or have close bacterial relatives that are capable of such metabolism, while many of the bacteria that lack the PTS either are strict aerobes or lack a complete glycolytic cycle.…”

Section: Numbers Of Pts Protein-encoding Genesmentioning

confidence: 88%

Comparative Genomic Analyses of the Bacterial Phosphotransferase System

Barabote

Saier

2005

Microbiol Mol Biol Rev

254

251

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SUMMARY We report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS). These included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. Homologues of PTS proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding PTS proteins has not occurred between the three domains of life. Of the 174 bacterial genomes (136 bacterial species) analyzed, 30 diverse species have no PTS homologues, and 29 species have cytoplasmic PTS phosphoryl transfer protein homologues but lack recognizable PTS permeases. These soluble homologues presumably function in regulation. The remaining 77 species possess all PTS proteins required for the transport and phosphorylation of at least one sugar via the PTS. Up to 3.2% of the genes in a bacterium encode PTS proteins. These homologues were analyzed for family association, range of protein types, domain organization, and organismal distribution. Different strains of a single bacterial species often possess strikingly different complements of PTS proteins. Types of PTS protein domain fusions were analyzed, showing that certain types of domain fusions are common, while others are rare or prohibited. Select PTS proteins were analyzed from different phylogenetic standpoints, showing that PTS protein phylogeny often differs from organismal phylogeny. The results document the frequent gain and loss of PTS protein-encoding genes and suggest that the lateral transfer of these genes within the bacterial domain has played an important role in bacterial evolution. Our studies provide insight into the development of complex multicomponent enzyme systems and lead to predictions regarding the types of protein-protein interactions that promote efficient PTS-mediated phosphoryl transfer.

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Biochemical Characterization of the Lysine Acetylation of Tyrosyl‐tRNA Synthetase in Escherichia coli

et al. 2017

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Aminoacyl-tRNA synthetases (aaRSs) play essential roles in protein synthesis. As a member of the aaRS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown in proteomic studies to be acetylated at multiple lysine residues. However, these putative acetylation targets have not yet been biochemically characterized. In this study, we applied a genetic-code-expansion strategy to site-specifically incorporate Nε-acetyl-L-lysine into selected positions of TyrRS for in vitro characterization. Enzyme assays demonstrated that acetylation at K85, K235, and K238 could impair the enzyme activity. In vitro deacetylation experiments showed that most acetylated lysine residues in TyrRS were sensitive to the E. coli deacetylase CobB but not YcgC. In vitro acetylation assays indicated that 25 members of the Gcn5-related N-acetyltransferase family in E. coli, including YfiQ, could not acetylate TyrRS efficiently, whereas TyrRS could be acetylated chemically by acetyl-CoA or acetyl-phosphate (AcP) only. Our in vitro characterization experiments indicated that lysine acetylation could be a possible mechanism for modulating aaRS enzyme activities, thus affecting translation.

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Functional genomic studies of dihydroxyacetone utilization in Escherichia coli

Abstract: Microbiology Comment provides a platform for readers of Microbiology to communicate their personal observations and opinions in a more informal way than through the submission of papers.

Cited by 25 publications

References 6 publications

How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria

How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria

Comparative Genomic Analyses of the Bacterial Phosphotransferase System

Biochemical Characterization of the Lysine Acetylation of Tyrosyl‐tRNA Synthetase in Escherichia coli

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