Identification and Characterization of an Archaeal Kojibiose Catabolic Pathway in the Hyperthermophilic Pyrococcus sp. Strain ST04

Jung, Jong‐Hyun; Seo, Dong-Ho; Holden, James F.; Park, Cheon-Seok

doi:10.1128/jb.01222-13

Cited by 13 publications

(5 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…YcjT is homologous to kojibiose phosphorylase from Thermoanerobacter brockii and Pyrococcus sp. Strain ST04 17,18 . Kojibiose phosphorylase can reversibly catabolize kojibiose to D-glucose and beta-D-glucose 1 phosphate.…”

Section: Resultsmentioning

confidence: 99%

Transcription factor YcjW controls the emergency H2S production in E. coli

et al. 2019

View full text Add to dashboard Cite

Prokaryotes and eukaryotes alike endogenously generate the gaseous molecule hydrogen sulfide (H 2 S). Bacterial H 2 S acts as a cytoprotectant against antibiotics-induced stress and promotes redox homeostasis. In E. coli , endogenous H 2 S production is primarily dependent on 3-mercaptopyruvate sulfurtransferase (3MST), encoded by mstA . Here, we show that cells lacking 3MST acquire a phenotypic suppressor mutation resulting in compensatory H 2 S production and tolerance to antibiotics and oxidative stress. Using whole genome sequencing, we identified a non-synonymous mutation within an uncharacterized LacI-type transcription factor, ycjW . We then mapped regulatory targets of YcjW and discovered it controls the expression of carbohydrate metabolic genes and thiosulfate sulfurtransferase PspE. Induction of pspE expression in the suppressor strain provides an alternative mechanism for H 2 S biosynthesis. Our results reveal a complex interaction between carbohydrate metabolism and H 2 S production in bacteria and the role, a hitherto uncharacterized transcription factor, YcjW, plays in linking the two.

show abstract

Section: Resultsmentioning

confidence: 99%

Transcription factor YcjW controls the emergency H2S production in E. coli

et al. 2019

View full text Add to dashboard Cite

show abstract

“…(59) The product of this reaction is β-D-glucose-1-P, which is the apparent substrate for the next enzyme in the pathway, YcjU. YcjT, which belongs to cog1554, shares 30% sequence identity with orthologs from Thermoanaerobacter brockii , Caldicellulosiruptor saccharolyticus , and an archaea, Pyrococcus sp .. (27, 28, 60) Kojibiose phosphorylases have previously been shown to transfer β-glucose-1-P to alternative acceptor substrates, apart from glucose. Our studies showed that among the monosaccharides tested in presence of β-D-glucose-1-P, only 1,5-anhydro-D-glucitol, L-sorbose, D-sorbitol or L-iditol can function as alternative substrates in the back reaction.…”

Section: Discussionmentioning

confidence: 99%

Discovery of a Kojibiose Phosphorylase in Escherichia coli K-12

2018

View full text Add to dashboard Cite

The substrate profiles for three uncharacterized enzymes (YcjM, YcjT, and YcjU) that are expressed from a cluster of 12 genes ( ycjM-W and ompG) of unknown function in Escherichia coli K-12 were determined. Through a comprehensive bioinformatic and steady-state kinetic analysis, the catalytic function of YcjT was determined to be kojibiose phosphorylase. In the presence of saturating phosphate and kojibiose (α-(1,2)-d-glucose-d-glucose), this enzyme catalyzes the formation of d-glucose and β-d-glucose-1-phosphate ( k = 1.1 s, K = 1.05 mM, and k/ K = 1.12 × 10 M s). Additionally, it was also shown that in the presence of β-d-glucose-1-phosphate, YcjT can catalyze the formation of other disaccharides using 1,5-anhydro-d-glucitol, l-sorbose, d-sorbitol, or l-iditol as a substitute for d-glucose. Kojibiose is a component of cell wall lipoteichoic acids in Gram-positive bacteria and is of interest as a potential low-calorie sweetener and prebiotic. YcjU was determined to be a β-phosphoglucomutase that catalyzes the isomerization of β-d-glucose-1-phosphate ( k = 21 s, K = 18 μM, and k/ K = 1.1 × 10 M s) to d-glucose-6-phosphate. YcjU was also shown to exhibit catalytic activity with β-d-allose-1-phosphate, β-d-mannose-1-phosphate, and β-d-galactose-1-phosphate. YcjM catalyzes the phosphorolysis of α-(1,2)-d-glucose-d-glycerate with a k = 2.1 s, K = 69 μM, and k/ K = 3.1 × 10 M s.

show abstract

“…Therefore, these would make interesting model enzymes for investigating the evolutionary relationship between glycoside hydrolases and phosphorylases [ 50 ], even though they only show 15–25% sequence identity. Besides its activity on kojibiose, Mm GH is also able to act on α-1,2-oligoglucans, an ability it shares with its phosphorylase counterparts [ 20 , 21 , 22 , 23 ]. Mm GH’s side-activity on nigerose (0.22% compared to kojibiose) did not come as a surprise either, as KPs have been reported to phosphorolyze nigerose with a similar relative activity (0.23–0.73%) [ 22 , 23 ].…”

Section: Discussionmentioning

confidence: 99%

“…Besides its activity on kojibiose, Mm GH is also able to act on α-1,2-oligoglucans, an ability it shares with its phosphorylase counterparts [ 20 , 21 , 22 , 23 ]. Mm GH’s side-activity on nigerose (0.22% compared to kojibiose) did not come as a surprise either, as KPs have been reported to phosphorolyze nigerose with a similar relative activity (0.23–0.73%) [ 22 , 23 ].…”

Section: Discussionmentioning

confidence: 99%

Discovery of a Kojibiose Hydrolase by Analysis of Specificity-Determining Correlated Positions in Glycoside Hydrolase Family 65

et al. 2021

View full text Add to dashboard Cite

The Glycoside Hydrolase Family 65 (GH65) is an enzyme family of inverting a-glucoside phosphorylases and hydrolases that currently contains 10 characterized enzyme specificities. However, its sequence diversity has never been studied in detail. Here, an in-silico analysis of correlated mutations was performed, revealing specificity-determining positions that facilitate annotation of the family’s phylogenetic tree. By searching these positions for amino acid motifs that do not match those found in previously characterized enzymes from GH65, several clades that may harbor new functions could be identified. Three enzymes from across these regions were expressed in E. coli and their substrate profile was mapped. One of those enzymes, originating from the bacterium Mucilaginibacter mallensis, was found to hydrolyze kojibiose and a-1,2-oligoglucans with high specificity. We propose kojibiose glucohydrolase as the systematic name and kojibiose hydrolase or kojibiase as the short name for this new enzyme. This work illustrates a convenient strategy for mapping the natural diversity of enzyme families and smartly mining the ever-growing number of available sequences in the quest for novel specificities.

show abstract

Identification and Characterization of an Archaeal Kojibiose Catabolic Pathway in the Hyperthermophilic Pyrococcus sp. Strain ST04

Cited by 13 publications

References 52 publications

Transcription factor YcjW controls the emergency H2S production in E. coli

Transcription factor YcjW controls the emergency H2S production in E. coli

Discovery of a Kojibiose Phosphorylase in Escherichia coli K-12

Discovery of a Kojibiose Hydrolase by Analysis of Specificity-Determining Correlated Positions in Glycoside Hydrolase Family 65

Contact Info

Product

Resources

About