Transaldolase/Glucose-6-phosphate Isomerase Bifunctional Enzyme and Ribulokinase as Factors to Increase Xylitol Production from<scp>D</scp>-Arabitol in<i>Gluconobacter oxydans</i>

Sugiyama, Masakazu; Suzuki, Shunichi; Tonouchi, Naoto; Yokozeki, Kenzo

doi:10.1271/bbb.67.2524

Cited by 12 publications

(7 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…7–9, 14: AroA/B or 15: AroA/E), to reasonable predictions (e.g. 11: a tRNA modification enzyme with riboflavin kinase, 16: GPI with transaldolase [ 23 ]), to highly surprising (e.g. 18: DnaK with Ser/Thr protein kinase) (see Additional File 6 , predicted).…”

Section: Resultsmentioning

confidence: 91%

Denoising inferred functional association networks obtained by gene fusion analysis

et al. 2007

View full text Add to dashboard Cite

BackgroundGene fusion detection – also known as the 'Rosetta Stone' method – involves the identification of fused composite genes in a set of reference genomes, which indicates potential interactions between its un-fused counterpart genes in query genomes. The precision of this method typically improves with an ever-increasing number of reference genomes.ResultsIn order to explore the usefulness and scope of this approach for protein interaction prediction and generate a high-quality, non-redundant set of interacting pairs of proteins across a wide taxonomic range, we have exhaustively performed gene fusion analysis for 184 genomes using an efficient variant of a previously developed protocol. By analyzing interaction graphs and applying a threshold that limits the maximum number of possible interactions within the largest graph components, we show that we can reduce the number of implausible interactions due to the detection of promiscuous domains. With this generally applicable approach, we generate a robust set of over 2 million distinct and testable interactions encompassing 696,894 proteins in 184 species or strains, most of which have never been the subject of high-throughput experimental proteomics. We investigate the cumulative effect of increasing numbers of genomes on the fidelity and quantity of predictions, and show that, for large numbers of genomes, predictions do not become saturated but continue to grow linearly, for the majority of the species. We also examine the percentage of component (and composite) proteins with relation to the number of genes and further validate the functional categories that are highly represented in this robust set of detected genome-wide interactions.ConclusionWe illustrate the phylogenetic and functional diversity of gene fusion events across genomes, and their usefulness for accurate prediction of protein interaction and function.

show abstract

Section: Resultsmentioning

confidence: 91%

Denoising inferred functional association networks obtained by gene fusion analysis

et al. 2007

View full text Add to dashboard Cite

show abstract

“…Our study suggested a possibility that NADH is generated through the pentose phosphate pathway (PPP), since the`xylitolincreasing factors' that we found and identied are enzymes of the PPP. 4) In this paper, we report investigation of the coenzyme specicity of key enzymes related to the oxidative PPP in G. oxydans. It was found that both glucose6phosphate dehydrogenase (G6PDH) and 6phosphogluconate dehydrogenase (6PGDH) have NAD W NADP dual coenzyme specicity, making it possible that one mechanism for NADH generation is the PPP in G. oxydans.…”

mentioning

confidence: 99%

“…Culture conditions and preparation of cellfree extracts were described in the accompanying report. 4) G6PDH and 6PGDH activities were measured at 309 C.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Coenzyme Specificity of Enzymes in the Oxidative Pentose Phosphate Pathway ofGluconobacter oxydans

Tonouchi

Sugiyama

Yokozeki

2003

Bioscience, Biotechnology, and Biochemistry

Self Cite

View full text Add to dashboard Cite

“…Ta activity was not detected when assaying just the assay mixture without added crude extracts or with crude cell extracts of a Ta negative C. glutamicum mutant Δtal. A possible explanation for the observed Ta activity in B. methanolicus PB1 and MGA3 could be the presence of potential bifunctional enzymes with transaldolase activity, such as glucose-6-phosphate isomerase/transaldolase described for Gluconobacter oxydans [64]. However, a BLAST search with the nucleotide and amino acid sequences of Ta from B. methanolicus PB1 and sequences of other Ta variants against the MGA genome sequence did not reveal any putative Ta genes or proteins.…”

Section: Enzyme Assays In Crude Extracts Demonstrated Ta Activities Fmentioning

confidence: 89%

Transaldolase in Bacillus methanolicus: biochemical characterization and biological role in ribulose monophosphate cycle

et al. 2020

View full text Add to dashboard Cite

Background: The Gram-positive facultative methylotrophic bacterium Bacillus methanolicus uses the sedoheptulose-1,7-bisphosphatase (SBPase) variant of the ribulose monophosphate (RuMP) cycle for growth on the C 1 carbon source methanol. Previous genome sequencing of the physiologically different B. methanolicus wild-type strains MGA3 and PB1 has unraveled all putative RuMP cycle genes and later, several of the RuMP cycle enzymes of MGA3 have been biochemically characterized. In this study, the focus was on the characterization of the transaldolase (Ta) and its possible role in the RuMP cycle in B. methanolicus. Results: The Ta genes of B. methanolicus MGA3 and PB1 were recombinantly expressed in Escherichia coli, and the gene products were purified and characterized. The PB1 Ta protein was found to be active as a homodimer with a molecular weight of 54 kDa and displayed K M of 0.74 mM and V max of 16.3 U/mg using Fructose-6 phosphate as the substrate. In contrast, the MGA3 Ta gene, which encodes a truncated Ta protein lacking 80 amino acids at the Nterminus, showed no Ta activity. Seven different mutant genes expressing various full-length MGA3 Ta proteins were constructed and all gene products displayed Ta activities. Moreover, MGA3 cells displayed Ta activities similar as PB1 cells in crude extracts. Conclusions:While it is well established that B. methanolicus can use the SBPase variant of the RuMP cycle this study indicates that B. methanolicus possesses Ta activity and may also operate the Ta variant of the RuMP.

show abstract

Transaldolase/Glucose-6-phosphate Isomerase Bifunctional Enzyme and Ribulokinase as Factors to Increase Xylitol Production fromD-Arabitol inGluconobacter oxydans

Cited by 12 publications

References 22 publications

Denoising inferred functional association networks obtained by gene fusion analysis

Denoising inferred functional association networks obtained by gene fusion analysis

Coenzyme Specificity of Enzymes in the Oxidative Pentose Phosphate Pathway ofGluconobacter oxydans

Transaldolase in Bacillus methanolicus: biochemical characterization and biological role in ribulose monophosphate cycle

Contact Info

Product

Resources

About