Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production in<i>Porphyromonas gingivalis</i>

Yamaguchi, Yasuo; Sato, Mitsunari; Nonaka, Takamasa; Hasegawa, Yoshinori; Kezuka, Yuichiro

doi:10.1080/20002297.2019.1588086

Cited by 7 publications

(9 citation statements)

References 69 publications

(100 reference statements)

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“…Very recently, importance of the phosphotransacetylase/acetate kinase pathway for ATP production was also described in Porphyromonas gingivalis which, similar to P. mucosa , belongs to the order Bacteroidales [ 73 , 74 , 75 , 76 ]. In the context of the central fermentation metabolism, it is interesting to note that P. mucosa encodes a malic enzyme (EC 1.1.1.40) and pyruvate, phosphate dikinase (EC 2.7.9.1) catalyzing the NAD(P) + dependent oxidative decarboxylation of malate to pyruvate [ 77 ] and the ATP-consuming conversion of pyruvate to phosphoenolpyruvate, respectively.…”

Section: Resultsmentioning

confidence: 99%

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

et al. 2020

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Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.

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Section: Resultsmentioning

confidence: 99%

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

et al. 2020

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“…Between the two domains is a cleft that is implicated in catalysis by other Ptas [ 29 , 30 ]. Although several water molecules are observed in this cleft, there was no evidence of substrates or products bound therein.…”

Section: Resultsmentioning

confidence: 99%

“…#6IOX; r.m.s.d. of 1.35 Å over 325 aligned C α ’s; [ 30 ]) and Bacillus subtilis (PDB Acc. #1TD9; r.m.s.d.…”

Section: Resultsmentioning

confidence: 99%

Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum

et al. 2023

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The mechanisms of energy generation and carbon-source utilization in the syphilis spirochete Treponema pallidum have remained enigmatic despite complete genomic sequence information. Whereas the bacterium harbors enzymes for glycolysis, the apparatus for more efficient use of glucose catabolites, namely the citric-acid cycle, is apparently not present. Yet, the organism’s energy needs likely exceed the modest output from glycolysis alone. Recently, building on our structure-function studies of T. pallidum lipoproteins, we proposed a “flavin-centric” metabolic lifestyle for the organism that partially resolves this conundrum. As a part of the hypothesis, we have proposed that T. pallidum contains an acetogenic energy-conservation pathway that catabolizes D-lactate, yielding acetate, reducing equivalents for the generation and maintenance of chemiosmotic potential, and ATP. We already have confirmed the D-lactate dehydrogenase activity in T. pallidum necessary for this pathway to operate. In the current study, we focused on another enzyme ostensibly involved in treponemal acetogenesis, phosphotransacetylase (Pta). This enzyme is putatively identified as TP0094 and, in this study, we determined a high-resolution (1.95 Å) X-ray crystal structure of the protein, finding that its fold comports with other known Pta enzymes. Further studies on its solution behavior and enzyme activity confirmed that it has the properties of a Pta. These results are consistent with the proposed acetogenesis pathway in T. pallidum, and we propose that the protein be referred to henceforth as TpPta.

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“…We then attempted to compare the Ca PTB structure with its structural homologues among phosphate acetyl/butyryltransferases, and the Dali server search showed that Ca PTB was highly structurally similar to members of acyltransferases such as phosphotransbutyrylase from L. monocytogenes ( Lm PTB, PDB code 3U9E) and E. faecalis ( Ef PTB, PDB code 1YCO) and phosphotransacetylase (PTA, phosphate acetyltransferase) from M. thermophila ( Mt PTA, PDB code 2AF3) [ 19 , 20 ] and P. gingivalis (PgPTA, PDB code 6IOX) [ 32 ] with RMSD for related elements ranging from 1.8 to 4.3 Å and 19-39% amino acid identity ( Fig. 1B ).…”

Section: Resultsmentioning

confidence: 99%

Crystal Structure and Molecular Mechanism of Phosphotransbutyrylase from Clostridium acetobutylicum

Kim

2021

J. Microbiol. Biotechnol.

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Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium Clostridium acetobutylicum has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase (phosphate butyryltransferase, PTB) plays a crucial role in butyrate metabolism by catalyzing the reversible conversion of butyryl-CoA into butyryl phosphate. Here, we report the crystal structure of PTB from the Clostridial host for ABE fermentation, C. acetobutylicum , ( Ca PTB) at a 2.9 Å resolution. The overall structure of the Ca PTB monomer is quite similar to those of other acyltransferases, with some regional structural differences. The monomeric structure of Ca PTB consists of two distinct domains, the N- and C-terminal domains. The active site cleft was formed at the interface between the two domains. Interestingly, the crystal structure of Ca PTB contained eight molecules per asymmetric unit, forming an octamer, and the size-exclusion chromatography experiment also suggested that the enzyme exists as an octamer in solution. The structural analysis of Ca PTB identifies the substrate binding mode of the enzyme and comparisons with other acyltransferase structures lead us to speculate that the enzyme undergoes a conformational change upon binding of its substrate.

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Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis

Cited by 7 publications

References 69 publications

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum

Crystal Structure and Molecular Mechanism of Phosphotransbutyrylase from Clostridium acetobutylicum

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