Seo H

References (15)

Title : Inactivated Split MERS-CoV Antigen Prevents Lethal Middle East Respiratory Syndrome Coronavirus Infections in Mice - Seo_2024_Vaccines.(Basel)_12_
Author(s) : Seo H , Jang Y , Kwak D
Ref : Vaccines (Basel) , 12 : , 2024
Abstract : Middle East respiratory syndrome coronavirus (MERS-CoV) causes fatal infections, with about 36% mortality in humans, and is endemic to the Middle East. MERS-CoV uses human dipeptidyl peptidase 4 (hDPP4) as a receptor for infection. Despite continued research efforts, no licensed vaccine is available for protection against this disease in humans. Therefore, this study sought to develop an inactivated fragmented MERS-CoV vaccine grown in Vero cells in an hDPP4-transgenic mouse model. Two-dose immunisation in mice with 15, 20, or 25 microg of spike proteins of inactivated split MERS-CoV antigens induced neutralising antibodies, with titres ranging from NT 80 to 1280. In addition, all immunised mice were completely protected, with no virus detection in tissues, weight loss, or mortality. The immunised splenocytes produced more cytokines that stimulate immune response (IFN-gamma and TNF-alpha) than those that regulate it (IL-4 and IL-10). Taken together, the inactivated fragmented MERS-CoV vaccine is effective for the protection of mice against lethal MERS-CoV. Thus, the inactivated fragmented MERS-CoV vaccine warrants further testing in other hosts.
ESTHER : Seo_2024_Vaccines.(Basel)_12_
PubMedSearch : Seo_2024_Vaccines.(Basel)_12_
PubMedID: 38675818

Title : Balance-directed protein engineering of IsPETase enhances both PET hydrolysis activity and thermostability - Lee_2023_bioRxiv__
Author(s) : Lee SH , Seo H , Hong H , Park J , Ki D , Kim M , Kim HJ , Kim KJ
Ref : Biorxiv , : , 2023
Abstract : A mesophilic PETase from Ideonella sakaiensis (IsPETase) has been shown to exhibit high PET hydrolysis activity, but its low thermostability limits its industrial applications. We herein developed an engineering strategy for IsPETase to enhance PET hydrolysis activity, thermostability, and protein folding of the enzyme. Balance-directed Z1-PETase variant outperforms the stability-directed Z2-PETase variant under both mesophilic and thermophilic conditions, although Z2-PETase exhibits higher thermostability than Z1-PETase. The Z1-PETase is also superior to Fast-PETase, Dura-PETase, and LC-CICCG in terms of depolymerization rate regardless of temperature conditions we tested. Thus, maintaining a balance between PET hydrolysis activity and thermostability is essential for the developmentof high-performance PET hydrolases. In a pH-stat bioreactor, Z1-PETase depolymerized >90% of both transparent and colored post-consumer PET powders within 24 and 8 hours at 40C and 55C, respectively, demonstrating that the balance-directed IsPETase variant produced herein may be applicable in the bio-recycling of PET.
ESTHER : Lee_2023_bioRxiv__
PubMedSearch : Lee_2023_bioRxiv__
Gene_locus related to this paper: idesa-peth

Title : Three-directional engineering of IsPETase with enhanced protein yield, activity, and durability - Lee_2023_J.Hazard.Mater_459_132297
Author(s) : Lee SH , Seo H , Hong H , Park J , Ki D , Kim M , Kim HJ , Kim KJ
Ref : J Hazard Mater , 459 :132297 , 2023
Abstract : The mesophilic PETase from Ideonella sakaiensis (IsPETase) has been shown to exhibit high PET hydrolysis activity, but its low stability limits its industrial applications. Here, we developed a variant, Z1-PETase, with enhanced soluble protein yield and durability while maintaining or improving activity at lower temperatures. The selected Z1-PETase not only exhibited a 20-fold improvement in soluble protein yield compared to the previously engineered IsPETase(S121E/D186H/S242T/N246D) (4p) variant, but also demonstrated a 30% increase in low-temperature activity at 40 degreesC, along with an 11 degreesC increase in its Tm(D) value. The PET depolymerization test across a temperature range low to high (30-70 degreesC) confirmed that Z1-PETase exhibits high accessibility of mesophilic PET hydrolase and rapid depolymerizing rate at higher temperature in accordance with the thermal behaviors of polymer and enzyme. Additionally, structural interpretation indicated that the stabilization of specific active site loops in Z1-PETase contributes to enhanced thermostability without adversely impacting enzymatic activity. In a pH-stat bioreactor, Z1-PETase depolymerized > 90% of both transparent and colored post-consumer PET powders within 24 and 8 h at 40 degreesC and 55 degreesC, respectively, demonstrating that the utility of this IsPETase variant in the bio-recycling of PET.
ESTHER : Lee_2023_J.Hazard.Mater_459_132297
PubMedSearch : Lee_2023_J.Hazard.Mater_459_132297
PubMedID: 37595467
Gene_locus related to this paper: idesa-peth

Title : Molecular mechanism underlying high-affinity terephthalate binding and conformational change of TBP from Ideonella sakaiensis - Lee_2023_Int.J.Biol.Macromol_243_125252
Author(s) : Lee SH , Seo H , Hong H , Kim M , Kim KJ
Ref : Int J Biol Macromol , 243 :125252 , 2023
Abstract : Ideonella sakaiensis is the bacterium that can survive by degrading polyethylene terephthalate (PET) plastic, and terephthalic acid (TPA) binding protein (IsTBP) is an essential periplasmic protein for uptake of TPA into the cytosol for complete degradation of PET. Here, we demonstrated that IsTBP has remarkably high specificity for TPA among 33 monophenolic compounds and two 1,6-dicarboxylic acids tested. Structural comparisons with 6-carboxylic acid binding protein (RpAdpC) and TBP from Comamonas sp. E6 (CsTphC) revealed the key structural features that contribute to high TPA specificity and affinity of IsTBP. We also elucidated the molecular mechanism underlying the conformational change upon TPA binding. In addition, we developed the IsTBP variant with enhanced TPA sensitivity, which can be expanded for the use of TBP as a biosensor for PET degradation.
ESTHER : Lee_2023_Int.J.Biol.Macromol_243_125252
PubMedSearch : Lee_2023_Int.J.Biol.Macromol_243_125252
PubMedID: 37295700

Title : Discovery and rational engineering of PET hydrolase with both mesophilic and thermophilic PET hydrolase properties - Hong_2023_Nat.Commun_14_4556
Author(s) : Hong H , Ki D , Seo H , Park J , Jang J , Kim KJ
Ref : Nat Commun , 14 :4556 , 2023
Abstract : Excessive polyethylene terephthalate (PET) waste causes a variety of problems. Extensive research focused on the development of superior PET hydrolases for PET biorecycling has been conducted. However, template enzymes employed in enzyme engineering mainly focused on IsPETase and leaf-branch compost cutinase, which exhibit mesophilic and thermophilic hydrolytic properties, respectively. Herein, we report a PET hydrolase from Cryptosporangium aurantiacum (CaPETase) that exhibits high thermostability and remarkable PET degradation activity at ambient temperatures. We uncover the crystal structure of CaPETase, which displays a distinct backbone conformation at the active site and residues forming the substrate binding cleft, compared with other PET hydrolases. We further develop a CaPETase(M9) variant that exhibits robust thermostability with a T(m) of 83.2 degreesC and 41.7-fold enhanced PET hydrolytic activity at 60 degreesC compared with CaPETase(WT). CaPETase(M9) almost completely decompose both transparent and colored post-consumer PET powder at 55 degreesC within half a day in a pH-stat bioreactor.
ESTHER : Hong_2023_Nat.Commun_14_4556
PubMedSearch : Hong_2023_Nat.Commun_14_4556
PubMedID: 37507390
Gene_locus related to this paper: 9actn-a0a1m7II12

Title : Rewiring metabolism of Clostridium thermocellum for consolidated bioprocessing of lignocellulosic biomass poplar to produce short-chain esters - Seo_2023_Bioresour.Technol__129263
Author(s) : Seo H , Singh P , Wyman CE , Cai CM , Trinh CT
Ref : Bioresour Technol , :129263 , 2023
Abstract : Consolidated bioprocessing (CBP) of lignocellulosic biomass uses cellulolytic microorganisms to enable enzyme production, saccharification, and fermentation to produce biofuels, biochemicals, and biomaterials in a single step. However, understanding and redirecting metabolisms of these microorganisms compatible with CBP are limited. Here, a cellulolytic thermophile Clostridium thermocellum was engineered and demonstrated to be compatible with CBP integrated with a Co-solvent Enhanced Lignocellulosic Fractionation (CELF) pretreatment for conversion of hardwood poplar into short-chain esters with industrial use as solvents, flavors, fragrances, and biofuels. The recombinant C. thermocellum engineered with deletion of carbohydrate esterases and stable overexpression of alcohol acetyltransferases improved ester production without compromised deacetylation activities. These esterases were discovered to exhibit promiscuous thioesterase activities and their deletion enhanced ester production by rerouting the electron and carbon metabolism. Ester production was further improved up to 80-fold and ester composition could be modulated by deleting lactate biosynthesis and using poplar with different pretreatment severity.
ESTHER : Seo_2023_Bioresour.Technol__129263
PubMedSearch : Seo_2023_Bioresour.Technol__129263
PubMedID: 37271458
Gene_locus related to this paper: clotm-c7hjn0

Title : Structural and functional characterization of an auxiliary domain-containing PET hydrolase from Burkholderiales bacterium - Sagong_2022_J.Hazard.Mater_429_128267
Author(s) : Sagong HY , Kim S , Lee D , Hong H , Lee SH , Seo H , Kim KJ
Ref : J Hazard Mater , 429 :128267 , 2022
Abstract : Biodegradation of polyethylene terephthalate (PET) is one of fundamental ways to solve plastic pollution. As various microbial hydrolases have an extra domain unlike PETase from Ideonella sakaiensis (IsPETase), research on the role of these extra domain in PET hydrolysis is crucial for the identification and selection of a novel PET hydrolase. Here, we report that a PET hydrolase from Burkholderiales bacterium RIFCSPLOWO2_02_FULL_57_36 (BbPETase) with an additional N-terminal domain (BbPETase(AND)) shows a similar hydrolysis activity toward microcrystalline PET and a higher thermal stability than IsPETase. Based on detailed structural comparisons between BbPETase and IsPETase, we generated the BbPETase(S335N/T338I/M363I/N365G) variant with an enhanced PET-degrading activity and thermal stability. We further revealed that BbPETase(AND) contributes to the thermal stability of the enzyme through close contact with the core domain, but the domain might hinder the adhesion of enzyme to PET substrate. We suggest that BbPETase is an enzyme in the evolution of efficient PET degradation and molecular insight into a novel PET hydrolase provides a novel strategy for the development of biodegradation of PET.
ESTHER : Sagong_2022_J.Hazard.Mater_429_128267
PubMedSearch : Sagong_2022_J.Hazard.Mater_429_128267
PubMedID: 35091192
Gene_locus related to this paper: 9burk-a0a1f4jxw8

Title : Implications for the PET decomposition mechanism through similarity and dissimilarity between PETases from Rhizobacter gummiphilus and Ideonella sakaiensis - Sagong_2021_J.Hazard.Mater_416_126075
Author(s) : Sagong HY , Son HF , Seo H , Hong H , Lee D , Kim KJ
Ref : J Hazard Mater , 416 :126075 , 2021
Abstract : The development of a superb polyethylene terephthalate (PET) hydrolyzing enzyme requires an accurate understanding of the PET decomposition mechanism. However, studies on PET degrading enzymes, including the PET hydrolase from Ideonella sakaiensis (IsPETase), have not provided sufficient knowledge of the molecular mechanisms for the hardly accessible substrate. Here, we report a novel PET hydrolase from Rhizobacter gummiphilus (RgPETase), which has a hydrolyzing activity similar to IsPETase toward microcrystalline PET but distinct behavior toward low crystallinity PET film. Structural analysis of RgPETase reveals that the enzyme shares the key structural features of IsPETase for high PET hydrolysis activity but has distinguished structures at the surface-exposed regions. RgPETase shows a unique conformation of the wobbling tryptophan containing loop (WW-loop) and change of the electrostatic surface charge on the loop dramatically affects the PET-degrading activity. We further show that effect of the electrostatic surface charge to the activity varies depending on locations. This work provides valuable information underlying the uncovered PET decomposition mechanism.
ESTHER : Sagong_2021_J.Hazard.Mater_416_126075
PubMedSearch : Sagong_2021_J.Hazard.Mater_416_126075
PubMedID: 34492896
Gene_locus related to this paper: 9burk-a0a1w6l588

Title : Decomposition of the PET Film by MHETase Using Exo-PETase Function - Sagong_2020_ACS.Catal_10_48050
Author(s) : Sagong HY , Seo H , Kim T , Son H , Joo S , Lee S , Kim S , Woo JS , Hwang S , Kim KJ
Ref : ACS Catal , 10 :4805 , 2020
Abstract : Monohydroxyethyl terephthalate (MHET) hydrolase (MHETase) is an enzyme known to be involved in the final degradation step of poly(ethylene terephthalate) (PET) by hydrolyzing MHET into terephthalic acid and ethylene glycol in Ideonella sakaiensis. Here, we report the extracellular production of MHETase in an active form with a proper folding. Based on the structural observations and biochemical experiments, we reveal that MHETase also functions as exo-PETase by hydrolyzing the synthesized PET pentamer. We further present that MHETase has a hydrolysis activity against the termini-generated PET film, demonstrating the exo-PETase function of the enzyme. We also develop a MHETase R411K/S416A/F424I variant with a higher BHET activity, and the variant exhibits an enhanced degradation activity against the PET film. Based on these results, we propose that MHETase plays several roles in the biodegradation of PET using the BHETase and exo-PETase activities as well as the MHET hydrolysis function
ESTHER : Sagong_2020_ACS.Catal_10_48050
PubMedSearch : Sagong_2020_ACS.Catal_10_48050
Gene_locus related to this paper: idesa-mheth

Title : Structural bioinformatics-based protein engineering of thermo-stable PETase from Ideonella sakaiensis - Son_2020_Enzyme.Microb.Technol_141_109656
Author(s) : Son HF , Joo S , Seo H , Sagong HY , Lee SH , Hong H , Kim KJ
Ref : Enzyme Microb Technol , 141 :109656 , 2020
Abstract : Poly(ethylene terephthalate) (PET), a widely used plastic around the world, causes various environmental and health problems. Several groups have been extensively conducting research to solve these problems through enzymatic degradation of PET at high temperatures around 70 degC. Recently, Ideonella sakaiensis, a bacterium that degrades PET at mild temperatures, has been newly identified, and further protein engineering studies on the PET degrading enzyme from the organism (IsPETase) have also been conducted to overcome the low thermal stability of the enzyme. In this study, we performed structural bioinformatics-based protein engineering of IsPETase to optimize the substrate binding site of the enzyme and developed two variants, IsPETase(S242T) and IsPETase(N246D), with higher enzymatic activity at both 25 and 37 degC compared with IsPETase(WT). We also developed the IsPETase(S121E/D186H/S242T/N246D) variant by integrating the S242T and N246D mutations into the previously reported IsPETase(S121E/D186H/R208A) variant. At the 37 degC incubation, the quadruple variant maintained the PET degradation activity for 20 days, unlike IsPETase(WT) that lost its activity within a day. Consequently, this study exhibited 58-fold increase in the activity compared with IsPETase(WT).
ESTHER : Son_2020_Enzyme.Microb.Technol_141_109656
PubMedSearch : Son_2020_Enzyme.Microb.Technol_141_109656
PubMedID: 33051015
Gene_locus related to this paper: idesa-mheth

Title : Reply to 'Conformational fitting of a flexible oligomeric substrate does not explain the enzymatic PET degradation' -
Author(s) : Seo H , Cho IJ , Joo S , Son HF , Sagong HY , Choi SY , Lee SY , Kim KJ
Ref : Nat Commun , 10 :5582 , 2019
PubMedID: 31811201

Title : Rational Protein Engineering of Thermo-Stable PETase from Ideonella sakaiensis for Highly Efficient PET Degradation - Son_2019_ACS.Catal_9_3519
Author(s) : Son HF , Cho IJ , Joo S , Seo H , Sagong HY , Choi SY , Lee SY , Kim KJ
Ref : ACS Catal , 9 :3519 , 2019
Abstract : Widespread utilization of polyethylene terephthalate (PET) has caused a variety of environmental and health problems; thus, the enzymatic degradation of PET can be a promising solution. Although PETase from Ideonalla sakaiensis (IsPETase) has been reported to have the highest PET degradation activity under mild conditions of all PET-degrading enzymes reported to date, its low thermal stability limits its ability for efficient and practical enzymatic degradation of PET. Using the structural information on IsPETase, we developed a rational protein engineering strategy using several IsPETase variants that were screened for high thermal stability to improve PET degradation activity. In particular, the IsPETaseS121E/D186H/R280A variant, which was designed to have a stabilized beta6-beta7 connecting loop and extended subsite IIc, had a Tm value that was increased by 8.81 C and PET degradation activity was enhanced by 14-fold at 40 C in comparison with IsPETaseWT. The designed structural modifications were further verified through structure determination of the variants, and high thermal stability was further confirmed by a heat-inactivation experiment. The proposed strategy and developed variants represent an important advancement for achieving the complete biodegradation of PET under mild conditions
ESTHER : Son_2019_ACS.Catal_9_3519
PubMedSearch : Son_2019_ACS.Catal_9_3519
Gene_locus related to this paper: idesa-mheth

Title : Production of extracellular PETase from Ideonella sakaiensis using sec-dependent signal peptides in E. coli - Seo_2019_Biochem.Biophys.Res.Commun_508_250
Author(s) : Seo H , Kim S , Son HF , Sagong HY , Joo S , Kim KJ
Ref : Biochemical & Biophysical Research Communications , 508 :250 , 2019
Abstract : Poly(ethylene terephthalate) (PET) is the most commonly used polyester polymer resin in fabrics and storage materials, and its accumulation in the environment is a global problem. The ability of PET hydrolase from Ideonella sakaiensis 201-F6 (IsPETase) to degrade PET at moderate temperatures has been studied extensively. However, due to its low structural stability and solubility, it is difficult to apply standard laboratory-level IsPETase expression and purification procedures in industry. To overcome this difficulty, the expression of IsPETase can be improved by using a secretion system. This is the first report on the production of an extracellular IsPETase, active against PET film, using Sec-dependent translocation signal peptides from E. coli. In this work, we tested the effects of fusions of the Sec-dependent and SRP-dependent signal peptides from E. coli secretory proteins into IsPETase, and successfully produced the extracellular enzyme using pET22b-SPMalE:IsPETase and pET22b-SPLamB:IsPETase expression systems. We also confirmed that the secreted IsPETase has PET-degradation activity. The work will be used for development of a new E. coli strain capable of degrading and assimilating PET in its culture medium.
ESTHER : Seo_2019_Biochem.Biophys.Res.Commun_508_250
PubMedSearch : Seo_2019_Biochem.Biophys.Res.Commun_508_250
PubMedID: 30477746
Gene_locus related to this paper: idesa-mheth

Title : Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation - Joo_2018_Nat.Commun_9_382
Author(s) : Joo S , Cho IJ , Seo H , Son HF , Sagong HY , Shin TJ , Choi SY , Lee SY , Kim KJ
Ref : Nat Commun , 9 :382 , 2018
Abstract : Plastics, including poly(ethylene terephthalate) (PET), possess many desirable characteristics and thus are widely used in daily life. However, non-biodegradability, once thought to be an advantage offered by plastics, is causing major environmental problem. Recently, a PET-degrading bacterium, Ideonella sakaiensis, was identified and suggested for possible use in degradation and/or recycling of PET. However, the molecular mechanism of PET degradation is not known. Here we report the crystal structure of I. sakaiensis PETase (IsPETase) at 1.5 A resolution. IsPETase has a Ser-His-Asp catalytic triad at its active site and contains an optimal substrate binding site to accommodate four monohydroxyethyl terephthalate (MHET) moieties of PET. Based on structural and site-directed mutagenesis experiments, the detailed process of PET degradation into MHET, terephthalic acid, and ethylene glycol is suggested. Moreover, other PETase candidates potentially having high PET-degrading activities are suggested based on phylogenetic tree analysis of 69 PETase-like proteins.
ESTHER : Joo_2018_Nat.Commun_9_382
PubMedSearch : Joo_2018_Nat.Commun_9_382
PubMedID: 29374183
Gene_locus related to this paper: idesa-peth

Title : Estrogen alters amyloid precursor protein as well as dendritic and cholinergic markers in a mouse model of Down syndrome - Granholm_2003_Hippocampus_13_905
Author(s) : Granholm AC , Sanders L , Seo H , Lin L , Ford K , Isacson O
Ref : Hippocampus , 13 :905 , 2003
Abstract : Individuals with Down syndrome (DS) develop the pathological hallmarks of Alzheimer's disease at an early age, later followed by memory decline and dementia. Women with DS are twice as likely to undergo early menopause, and levels of estradiol correlate with onset of cognitive decline in these women. We have demonstrated that a mouse model of DS, mice with segmental trisomy of chromosome 16 (Ts65Dn), develop a significant deficit in both reference and working memory as young adults (6-10 months of age), coupled with phenotypic loss of cholinergic neurons in the basal forebrain and altered growth factor levels. In the present study we examined cholinergic and dendritic markers in the hippocampal formation and levels of the amyloid precursor protein (APP) in different brain regions of Ts65Dn mice treated with estradiol for 60 days. The density of the dendritic marker Map2 was significantly decreased in the hippocampal formation of middle-aged trisomic mice (9-15 months old), and the density of cholinergic neurites (acetylcholinesterase [AChE] histochemistry) was also decreased in specific layers of the hippocampus. Treatment with 17beta-estradiol alleviated the decreases in Map2 and AChE staining, but had no effect on full-length APP levels in the hippocampus. In contrast, a main effect of treatment on APP levels in the striatum was noted, with significant elevations observed in controls and trisomics. These findings demonstrate that estrogen can alleviate deficits in cholinergic and dendritic elements in the hippocampal formation and further strengthens the rationale to explore estrogen replacement therapy in women with DS.
ESTHER : Granholm_2003_Hippocampus_13_905
PubMedSearch : Granholm_2003_Hippocampus_13_905
PubMedID: 14750653