1
|
Zhang W, Ren H, Chen J, Ni D, Xu W, Mu W. Enhancement of the d-Allulose 3-Epimerase Expression in Bacillus subtilis through Both Transcriptional and Translational Regulations. J Agric Food Chem 2024; 72:8052-8059. [PMID: 38563420 DOI: 10.1021/acs.jafc.4c01122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
d-Allulose, a functional bulk sweetener, has recently attracted increasing attention because of its low-caloric-ness properties and diverse health effects. d-Allulose is industrially produced by the enzymatic epimerization of d-fructose, which is catalyzed by ketose 3-epimerase (KEase). In this study, the food-grade expression of KEase was studied using Bacillus subtills as the host. Clostridium sp. d-allulose 3-epimerase (Clsp-DAEase) was screened from nine d-allulose-producing KEases, showing better potential for expression in B. subtills WB600. Promoter-based transcriptional regulation and N-terminal coding sequence (NCS)-based translational regulation were studied to enhance the DAEase expression level. In addition, the synergistic effect of promoter and NCS on the Clsp-DAEase expression was studied. Finally, the strain with the combination of a PHapII promoter and gln A-Up NCS was selected as the best Clsp-DAEase-producing strain. It efficiently produced Clsp-DAEase with a total activity of 333.2 and 1860.6 U/mL by shake-flask and fed-batch cultivations, respectively.
Collapse
Affiliation(s)
- Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hu Ren
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - JiaJun Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Dawei Ni
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wei Xu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| |
Collapse
|
2
|
McGary LC, Fetter CM, Gu M, Hamilton MC, Kumar H, Kuehm OP, Douglas CD, Bearne SL. Interrogating l-fuconate dehydratase with tartronate and 3-hydroxypyruvate reveals subtle differences within the mandelate racemase-subgroup of the enolase superfamily. Arch Biochem Biophys 2024; 754:109924. [PMID: 38354877 DOI: 10.1016/j.abb.2024.109924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Enzymes of the enolase superfamily share a conserved structure and a common partial reaction (i.e., metal-assisted, Brønsted base-catalyzed enol(ate) formation). The architectures of the enolization apparatus at the active sites of the mandelate racemase (MR)-subgroup members MR and l-fuconate dehydratase (FucD) are almost indistinguishable at the structural level. Tartronate and 3-hydroxypyruvate (3-HP) recognize the enolization apparatus and can be used to interrogate the active sites for differences that may not be apparent from structural data. We report a circular dichroism-based assay of FucD activity that monitors the change in ellipticity at 216 nm (Δ[Θ]S-P = 8985 ± 87 deg cm2 mol-1) accompanying the conversion of l-fuconate to 2-keto-3-deoxy-l-fuconate. Tartronate was a linear mixed-type inhibitor of FucD (Ki = 8.4 ± 0.7 mM, αKi = 63 ± 11 mM), binding 18-fold weaker than l-fuconate, compared with 2-fold weaker binding of tartronate by MR relative to mandelate. 3-HP irreversibly inactivated FucD (kinact/KI = 0.018 ± 0.002 M-1s-1) with an efficiency that was ∼4.6 × 103-fold less than that observed with MR. The inactivation arose predominantly from modifications at multiple sites and Tris-HCl, but not l-fuconate, afforded protection against inactivation. Similar to the reaction of 3-HP with MR, 3-HP modified the Brønsted base catalyst (Lys 220) at the active site of FucD, which was facilitated by the Brønsted acid catalyst His 351. Thus, the interactions of tartronate and 3-HP with MR and FucD revealed differences in binding affinity and reactivity that differentiated between the enzymes' enolization apparatuses.
Collapse
Affiliation(s)
- Laura C McGary
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Christopher M Fetter
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Minglu Gu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Meghan C Hamilton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Himank Kumar
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Oliver P Kuehm
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Colin D Douglas
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
| |
Collapse
|
3
|
Xiao Z, Zhao Z, Jiang B, Chen J. Enhancing enzyme immobilization: Fabrication of biosilica-based organic-inorganic composite carriers for efficient covalent binding of D-allulose 3-epimerase. Int J Biol Macromol 2024; 265:130980. [PMID: 38508569 DOI: 10.1016/j.ijbiomac.2024.130980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
D-allulose, an ideal low-calorie sweetener, is primarily produced through the isomerization of d-fructose using D-allulose 3-epimerase (DAE; EC 5.1.3.30). Addressing the gap in available immobilized DAE enzymes for scalable commercial D-allulose production, three core-shell structured organic-inorganic composite silica-based carriers were designed for efficient covalent immobilization of DAE. Natural inorganic diatomite was used as the core, while 3-aminopropyltriethoxysilane (APTES), polyethyleneimine (PEI), and chitosan organic layers were coated as the shells, respectively. These tailored carriers successfully formed robust covalent bonds with DAE enzyme conjugates, cross-linked via glutaraldehyde, and demonstrated enzyme activities of 372 U/g, 1198 U/g, and 381 U/g, respectively. These immobilized enzymes exhibited an expanded pH tolerance and improved thermal stability compared to free DAE. Particularly, the modified diatomite with PEI exhibited a higher density of binding sites than the other carriers and the PEI-coated immobilized DAE enzyme retained 70.4 % of its relative enzyme activity after ten cycles of reuse. This study provides a promising method for DAE immobilization, underscoring the potential of using biosilica-based organic-inorganic composite carriers for the development of robust enzyme systems, thereby advancing the production of value-added food ingredients like D-allulose.
Collapse
Affiliation(s)
- Ziqun Xiao
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zishen Zhao
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Bo Jiang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Jingjing Chen
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| |
Collapse
|
4
|
Coppinger MN, Laramore K, Popham DL, Stabb EV. A prototrophic suppressor of a Vibrio fischeri D-glutamate auxotroph reveals a member of the periplasmic broad-spectrum racemase family (BsrF). J Bacteriol 2024; 206:e0033323. [PMID: 38411059 PMCID: PMC10955857 DOI: 10.1128/jb.00333-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Although bacterial peptidoglycan (PG) is highly conserved, some natural variations in PG biosynthesis and structure have evolved. Understanding the mechanisms and limits of such variation will inform our understanding of antibiotic resistance, innate immunity, and the evolution of bacteria. We have explored the constraints on PG evolution by blocking essential steps in PG biosynthesis in Vibrio fischeri and then selecting mutants with restored prototrophy. Here, we attempted to select prototrophic suppressors of a D-glutamate auxotrophic murI racD mutant. No suppressors were isolated on unsupplemented lysogeny broth salts (LBS), despite plating >1011 cells, nor were any suppressors generated through mutagenesis with ethyl methanesulfonate. A single suppressor was isolated on LBS supplemented with iso-D-gln, although the iso-D-gln subsequently appeared irrelevant. This suppressor has a genomic amplification formed by the creation of a novel junction that fuses proB to a gene encoding a putative broad-spectrum racemase of V. fischeri, bsrF. An engineered bsrF allele lacking the putative secretion signal (ΔSS-bsrF) also suppressed D-glu auxotrophy, resulting in PG that was indistinguishable from the wild type. The ΔSS-bsrF allele similarly suppressed the D-alanine auxotrophy of an alr mutant and restored prototrophy to a murI alr double mutant auxotrophic for both D-ala and D-glu. The ΔSS-bsrF allele increased resistance to D-cycloserine but had no effect on sensitivity to PG-targeting antibiotics penicillin, ampicillin, or vancomycin. Our work helps define constraints on PG evolution and reveals a periplasmic broad-spectrum racemase in V. fischeri that can be co-opted for PG biosynthesis, with concomitant D-cycloserine resistance. IMPORTANCE D-Amino acids are used and produced by organisms across all domains of life, but often, their origins and roles are not well understood. In bacteria, D-ala and D-glu are structural components of the canonical peptidoglycan cell wall and are generated by dedicated racemases Alr and MurI, respectively. The more recent discovery of additional bacterial racemases is broadening our view and deepening our understanding of D-amino acid metabolism. Here, while exploring alternative PG biosynthetic pathways in Vibrio fischeri, we unexpectedly shed light on an unusual racemase, BsrF. Our results illustrate a novel mechanism for the evolution of antibiotic resistance and provide a new avenue for exploring the roles of non-canonical racemases and D-amino acids in bacteria.
Collapse
Affiliation(s)
- Macey N. Coppinger
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Department of Biological Sciences, University of Illinois, Chicago, Illinois, USA
| | - Kathrin Laramore
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Eric V. Stabb
- Department of Biological Sciences, University of Illinois, Chicago, Illinois, USA
| |
Collapse
|
5
|
Jiang Y, Li X, Liu Q, Lei G, Wu C, Chen L, Zhao Y, Hu Y, Xian H, Mao R. Apolipoprotein A-I Binding Protein Inhibits the Formation of Infantile Hemangioma through Cholesterol-Regulated Hypoxia-Inducible Factor 1α Activation. J Invest Dermatol 2024; 144:645-658.e7. [PMID: 37832842 DOI: 10.1016/j.jid.2023.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 10/15/2023]
Abstract
Infantile hemangioma (IH) is the most frequent vascular tumor of infancy with unclear pathogenesis; disordered angiogenesis is considered to be involved in its formation. Apolipoprotein A-I binding protein (AIBP)-also known as NAXE (NAD [P]HX epimerase)-a regulator of cholesterol metabolism, plays a critical role in the pathological angiogenesis of mammals. In this study, we found that AIBP had much lower expression levels in both tissues from patients with IH and hemangioma endothelial cells (HemECs) than in adjacent normal tissues and human dermal vascular endothelial cells, respectively. Knockout of NAXE by CRISPR-Cas9 in HemECs enhanced tube formation and migration, and NAXE overexpression impaired tube formation and migration of HemECs. Interestingly, AIBP suppressed the proliferation of HemECs in hypoxia. We then found that reduced expression of AIBP correlated with increased hypoxia-inducible factor 1α levels in tissues from patients with IH and HemECs. Further mechanistic investigation demonstrated that AIBP disrupted hypoxia-inducible factor 1α signaling through cholesterol metabolism under hypoxia. Notably, AIBP significantly inhibited the development of IH in immunodeficient mice. Furthermore, using the validated mouse endothelial cell (ie, EOMA cells) and Naxe-/- mouse models, we demonstrated that both endogenous AIBP from tumors and AIBP in the tumor microenvironment limit the formation of hemangioma. These findings suggested that AIBP was a player in the pathogenesis of IH and could be a potential pharmacological target for treating IH.
Collapse
Affiliation(s)
- Yongying Jiang
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China
| | - Xingjuan Li
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China
| | - Qin Liu
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China
| | - Gongyun Lei
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China
| | - Changyue Wu
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong University, Jiangsu, China
| | - Long Chen
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Nantong University, Jiangsu, China
| | - Yinshuang Zhao
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Nantong University, Jiangsu, China
| | - Yae Hu
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China
| | - Hua Xian
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Nantong University, Jiangsu, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China.
| |
Collapse
|
6
|
Han SW, Jang Y, Kook J, Jang J, Shin JS. Reprogramming biocatalytic futile cycles through computational engineering of stereochemical promiscuity to create an amine racemase. Nat Commun 2024; 15:49. [PMID: 38169460 PMCID: PMC10761954 DOI: 10.1038/s41467-023-44218-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Repurposing the intrinsic properties of natural enzymes can offer a viable solution to current synthetic challenges through the development of novel biocatalytic processes. Although amino acid racemases are ubiquitous in living organisms, an amine racemase (AR) has not yet been discovered despite its synthetic potential for producing chiral amines. Here, we report the creation of an AR based on the serendipitous discovery that amine transaminases (ATAs) can perform stereoinversion of 2-aminobutane. Kinetic modeling revealed that the unexpected off-pathway activity results from stereochemically promiscuous futile cycles due to incomplete stereoselectivity for 2-aminobutane. This finding motivated us to engineer an S-selective ATA through in silico alanine scanning and empirical combinatorial mutations, creating an AR with broad substrate specificity. The resulting AR, carrying double point mutations, enables the racemization of both enantiomers of diverse chiral amines in the presence of a cognate ketone. This strategy may be generally applicable to a wide range of transaminases, paving the way for the development of new-to-nature racemases.
Collapse
Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Department of Biotechnology, Konkuk University, Chungju, South Korea
| | - Youngho Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jihyun Kook
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jeesu Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea.
| |
Collapse
|
7
|
Qi H, Wang T, Li H, Li C, Guan L, Liu W, Wang J, Lu F, Mao S, Qin HM. Sequence- and Structure-Based Mining of Thermostable D-Allulose 3-Epimerase and Computer-Guided Protein Engineering To Improve Enzyme Activity. J Agric Food Chem 2023; 71:18431-18442. [PMID: 37970673 DOI: 10.1021/acs.jafc.3c07204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
D-Allulose, a functional sweetener, can be synthesized from fructose using D-allulose 3-epimerase (DAEase). Nevertheless, a majority of the reported DAEases have inadequate stability under harsh industrial reaction conditions, which greatly limits their practical applications. In this study, big data mining combined with a computer-guided free energy calculation strategy was employed to discover a novel DAEase with excellent thermostability. Consensus sequence analysis of flexible regions and comparison of binding energies after substrate docking were performed using phylogeny-guided big data analyses. TtDAE from Thermogutta terrifontis was the most thermostable among 358 candidate enzymes, with a half-life of 32 h at 70 °C. Subsequently, structure-guided virtual screening and a customized strategy based on a combinatorial active-site saturation test/iterative saturation mutagenesis were utilized to engineer TtDAE. Finally, the catalytic activity of the M4 variant (P105A/L14C/T63G/I65A) was increased by 5.12-fold. Steered molecular dynamics simulations indicated that M4 had an enlarged substrate-binding pocket, which enhanced the fit between the enzyme and the substrate. The approach presented here, combining DAEases mining with further rational modification, provides guidance for obtaining promising catalysts for industrial-scale production.
Collapse
Affiliation(s)
- Hongbin Qi
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Tong Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Huimin Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Lijun Guan
- Institute of Food Processing, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jianwen Wang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| |
Collapse
|
8
|
Xiao W, Tsunoda T, Maruyama C, Hamano Y, Ogasawara Y, Dairi T. Peptide epimerase-dehydratase complex responsible for biosynthesis of the linaridin class ribosomal peptides. Biosci Biotechnol Biochem 2023; 87:1316-1322. [PMID: 37541960 DOI: 10.1093/bbb/zbad106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/29/2023] [Indexed: 08/06/2023]
Abstract
Grisemycin, salinipeptin, and cypemycin belong to the linaridin class of ribosomally synthesized and posttranslationally modified peptides that contain multiple dehydrobutyrine and D-amino acid residues. The biosynthetic gene clusters of these linaridins lack obvious candidate genes for the dehydratase and epimerase required to introduce dehydrobutyrine and D-amino acid residues, respectively. However, we previously demonstrated that the grisemycin (grm) cluster contained cryptic dehydratase and epimerase genes by heterologous expression of this biosynthetic gene cluster in Streptomyces lividans and proposed that two genes (grmH and grmL) with unknown functions catalyze dehydration and epimerization reactions. In this study, we confirmed that both GrmH and GrmL, which were shown to constitute a protein complex by a co-purification experiment, were required to catalyze the dehydration, epimerization, and proteolytic cleavage of a precursor peptide GrmA by in vivo experiments. Furthermore, we demonstrated that GrmH/GrmL complex accepted salinipeptin and cypemycin precursor peptides, which possess three additional amino acids.
Collapse
Affiliation(s)
- Wanlu Xiao
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Takeshi Tsunoda
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, Yoshida-Gun, Fukui, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, Yoshida-Gun, Fukui, Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| |
Collapse
|
9
|
Thoden JB, McKnight JO, Kroft CW, Jast JDT, Holden HM. Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis. J Biol Chem 2023; 299:105200. [PMID: 37660908 PMCID: PMC10622841 DOI: 10.1016/j.jbc.2023.105200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/18/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023] Open
Abstract
The sugar, 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, was first identified ∼40 years ago in the O-antigen of Pseudomonas aeruginosa O:3,a,d. Since then, it has been observed on the O-antigens of various pathogenic Gram-negative bacteria including Bordetella pertussis, Escherichia albertii, and Pseudomonas mediterranea. Previous studies have established that five enzymes are required for its biosynthesis beginning with uridine dinucleotide (UDP)-N-acetyl-d-glucosamine (UDP-GlcNAc). The final step in the pathway is catalyzed by a 2-epimerase, which utilizes UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid as its substrate. Curious as to whether this biochemical pathway is found in extreme thermophiles, we examined the published genome sequence for Thermus thermophilus HB27 and identified five ORFs that could possibly encode for the required enzymes. The focus of this investigation is on the ORF WP_011172736, which we demonstrate encodes for a 2-epimerase. For this investigation, ten high resolution X-ray crystallographic structures were determined to resolutions of 2.3 Å or higher. The models have revealed the manner in which the 2-epimerase anchors its UDP-sugar substrate as well as its UDP-sugar product into the active site. In addition, this study reveals for the first time the manner in which any sugar 2-epimerase can simultaneously bind UDP-sugars in both the active site and the allosteric binding region. We have also demonstrated that the T. thermophilus enzyme is allosterically regulated by UDP-GlcNAc. Whereas the sugar 2-epimerases that function on UDP-GlcNAc have been the focus of past biochemical and structural analyses, this is the first detailed investigation of a 2-epimerase that specifically utilizes UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid as its substrate.
Collapse
Affiliation(s)
- James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - James O McKnight
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Charles W Kroft
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Joshua D T Jast
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA.
| |
Collapse
|
10
|
He F, Jiang H, Peng C, Wang T, Xiao R, Chen M, Song N, Du Z, Wang H, Ding X, Shao Y, Fang J, Zang Y, Hua R, Li J, Ding K. Hepatic glucuronyl C5-epimerase combats obesity by stabilising GDF15. J Hepatol 2023; 79:605-617. [PMID: 37217020 DOI: 10.1016/j.jhep.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND & AIMS Disturbed hepatic metabolism frequently results in excessive lipid accumulation in the adipose tissue. However, the specific role of the liver-adipose axis in maintaining lipid homeostasis, as well as the underlying mechanism, has not yet been fully elucidated. In this study, we investigated the role of hepatic glucuronyl C5-epimerase (Glce) in the progression of obesity. METHODS We determined the association between the expression of hepatic Glce and body mass index (BMI) in obese patients. Obesity models were established in hepatic Glce-knockout and wild-type mice fed a high-fat diet (HFD) to understand the effect of Glce on obesity development. The role of Glce in the progression of disrupted hepatokine secretion was examined via secretome analysis. RESULTS Hepatic Glce expression was inversely correlated with BMI in obese patients. Moreover, Glce level was found to be decreased in the liver of a HFD murine model. Hepatic Glce deficiency led to impaired thermogenesis in adipose tissue and exacerbated HFD-induced obesity. Interestingly, decreased level of growth differentiation factor 15 (GDF15) was observed in the culture medium of Glce-knockout mouse hepatocytes. Treatment with recombinant GDF15 obstructed obesity progression derived from the absence of hepatic Glce, similar to the effect of Glce or its inactive mutant overexpressed both in vitro and in vivo. Furthermore, liver Glce deficiency led to diminished production and increased degradation of mature GDF15, resulting in reduced hepatic GDF15 secretion. CONCLUSIONS Hepatic Glce deficiency facilitated obesity development, and decreased Glce expression further reduced hepatic secretion of GDF15, thereby perturbing lipid homeostasis in vivo. Therefore, the novel Glce-GDF15 axis plays an important role in maintaining energy balance and may act as a potential target for combating obesity. IMPACT AND IMPLICATIONS Evidence suggests that GDF15 plays a key role in hepatic metabolism; however, the molecular mechanism for regulating its expression and secretion is largely unknown. Our work observes that hepatic Glce, as a key Golgi-localised epimerase, may work on the maturation and post-translational regulation of GDF15. Hepatic Glce deficiency reduces the production of mature GDF15 protein and facilitates its ubiquitination, resulting in the aggravation of obesity development. This study sheds light on the new function and mechanism of the Glce-GDF15 axis in lipid metabolism and provides a potential therapeutic target against obesity.
Collapse
Affiliation(s)
- Fei He
- Carbohydrate Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Haowen Jiang
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chang Peng
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Wang
- Carbohydrate Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Rongrong Xiao
- Carbohydrate Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Meilin Chen
- Carbohydrate Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Nixue Song
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyun Du
- Carbohydrate Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hanlin Wang
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Ding
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yikai Shao
- Center for Obesity and Metabolic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Jianping Fang
- Carbohydrate Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yi Zang
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China; Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Rong Hua
- Center for Obesity and Metabolic Surgery, Huashan Hospital of Fudan University, Shanghai, China.
| | - Jia Li
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China; Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
| | - Kan Ding
- Carbohydrate Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
| |
Collapse
|
11
|
Tan JH, Chen A, Bi J, Lim YH, Wong FT, Ow DSW. The Engineering, Expression, and Immobilization of Epimerases for D-allulose Production. Int J Mol Sci 2023; 24:12703. [PMID: 37628886 PMCID: PMC10454905 DOI: 10.3390/ijms241612703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The rare sugar D-allulose is a potential replacement for sucrose with a wide range of health benefits. Conventional production involves the employment of the Izumoring strategy, which utilises D-allulose 3-epimerase (DAEase) or D-psicose 3-epimerase (DPEase) to convert D-fructose into D-allulose. Additionally, the process can also utilise D-tagatose 3-epimerase (DTEase). However, the process is not efficient due to the poor thermotolerance of the enzymes and low conversion rates between the sugars. This review describes three newly identified DAEases that possess desirable properties for the industrial-scale manufacturing of D-allulose. Other methods used to enhance process efficiency include the engineering of DAEases for improved thermotolerance or acid resistance, the utilization of Bacillus subtilis for the biosynthesis of D-allulose, and the immobilization of DAEases to enhance its activity, half-life, and stability. All these research advancements improve the yield of D-allulose, hence closing the gap between the small-scale production and industrial-scale manufacturing of D-allulose.
Collapse
Affiliation(s)
- Jin Hao Tan
- Microbial Cell Bioprocessing, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668, Singapore;
| | - Anqi Chen
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (A*STAR), Singapore 138665, Singapore; (A.C.); (F.T.W.)
| | - Jiawu Bi
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore 117542, Singapore
| | - Yee Hwee Lim
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (A*STAR), Singapore 138665, Singapore; (A.C.); (F.T.W.)
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore 117597, Singapore
| | - Fong Tian Wong
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (A*STAR), Singapore 138665, Singapore; (A.C.); (F.T.W.)
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
| | - Dave Siak-Wei Ow
- Microbial Cell Bioprocessing, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668, Singapore;
| |
Collapse
|
12
|
Nakashima Y, Kawakami A, Ogasawara Y, Maeki M, Tokeshi M, Dairi T, Morita H. Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism. Nat Commun 2023; 14:4752. [PMID: 37550286 PMCID: PMC10406935 DOI: 10.1038/s41467-023-40232-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 07/13/2023] [Indexed: 08/09/2023] Open
Abstract
The lasso peptide MS-271 is a ribosomally synthesized and post-translationally modified peptide (RiPP) consisting of 21 amino acids with D-tryptophan at the C-terminus, and is derived from the precursor peptide MslA. MslH, encoded in the MS-271 biosynthetic gene cluster (msl), catalyzes the epimerization at the Cα center of the MslA C-terminal Trp21, leading to epi-MslA. The detailed catalytic process, including the catalytic site and cofactors, has remained enigmatic. Herein, based on X-ray crystallographic studies in association with MslA core peptide analogues, we show that MslH is a metallo-dependent peptide epimerase with a calcineurin-like fold. The crystal structure analysis, followed by site-directed mutagenesis, docking simulation, and ICP-MS studies demonstrate that MslH employs acid/base chemistry to facilitate the reversible epimerization of the C-terminal Trp21 of MslA, by utilizing two pairs of His/Asp catalytic residues that are electrostatically tethered to a six-coordination motif with a Ca(II) ion via water molecules.
Collapse
Affiliation(s)
- Yu Nakashima
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama, 930-0194, Japan
| | - Atsushi Kawakami
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Masatoshi Maeki
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Manabu Tokeshi
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.
| | - Hiroyuki Morita
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama, 930-0194, Japan.
| |
Collapse
|
13
|
Andresen S, de Mojana di Cologna N, Archer-Hartmann S, Rogers AM, Samaddar S, Ganguly T, Black IM, Glushka J, Ng KKS, Azadi P, Lemos JA, Abranches J, Szymanski CM. Involvement of the Streptococcus mutans PgfE and GalE 4-epimerases in protein glycosylation, carbon metabolism, and cell division. Glycobiology 2023; 33:245-259. [PMID: 36637425 PMCID: PMC10114643 DOI: 10.1093/glycob/cwad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Streptococcus mutans is a key pathogen associated with dental caries and is often implicated in infective endocarditis. This organism forms robust biofilms on tooth surfaces and can use collagen-binding proteins (CBPs) to efficiently colonize collagenous substrates, including dentin and heart valves. One of the best characterized CBPs of S. mutans is Cnm, which contributes to adhesion and invasion of oral epithelial and heart endothelial cells. These virulence properties were subsequently linked to post-translational modification (PTM) of the Cnm threonine-rich repeat region by the Pgf glycosylation machinery, which consists of 4 enzymes: PgfS, PgfM1, PgfE, and PgfM2. Inactivation of the S. mutans pgf genes leads to decreased collagen binding, reduced invasion of human coronary artery endothelial cells, and attenuated virulence in the Galleria mellonella invertebrate model. The present study aimed to better understand Cnm glycosylation and characterize the predicted 4-epimerase, PgfE. Using a truncated Cnm variant containing only 2 threonine-rich repeats, mass spectrometric analysis revealed extensive glycosylation with HexNAc2. Compositional analysis, complemented with lectin blotting, identified the HexNAc2 moieties as GlcNAc and GalNAc. Comparison of PgfE with the other S. mutans 4-epimerase GalE through structural modeling, nuclear magnetic resonance, and capillary electrophoresis demonstrated that GalE is a UDP-Glc-4-epimerase, while PgfE is a GlcNAc-4-epimerase. While PgfE exclusively participates in protein O-glycosylation, we found that GalE affects galactose metabolism and cell division. This study further emphasizes the importance of O-linked protein glycosylation and carbohydrate metabolism in S. mutans and identifies the PTM modifications of the key CBP, Cnm.
Collapse
Affiliation(s)
- Silke Andresen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | | | | | - Ashley M Rogers
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Sandip Samaddar
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32603, USA
| | - Tridib Ganguly
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32603, USA
| | - Ian M Black
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - John Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Kenneth K S Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - José A Lemos
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32603, USA
| | - Jacqueline Abranches
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32603, USA
| | - Christine M Szymanski
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
14
|
Xiang DF, Ghosh MK, Riegert AS, Thoden JB, Holden HM, Raushel FM. Bifunctional Epimerase/Reductase Enzymes Facilitate the Modulation of 6-Deoxy-Heptoses Found in the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry 2023; 62:134-144. [PMID: 36534477 PMCID: PMC9838653 DOI: 10.1021/acs.biochem.2c00633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Campylobacter jejuni is a human pathogen and the leading cause of food poisoning in the United States and Europe. Surrounding the exterior surface of this bacterium is a capsular polysaccharide (CPS) that consists of a repeating sequence of common and unusual carbohydrate segments. At least 10 different heptose sugars have thus far been identified in the various strains of C. jejuni. The accepted biosynthetic pathway for the construction of the 6-deoxy-heptoses begins with the 4,6-dehydration of GDP-d-glycero-d-manno-heptose by a dehydratase, followed by an epimerase that racemizes C3 and/or C5 of the product GDP-6-deoxy-4-keto-d-lyxo-heptose. In the final step, a C4-reductase catalyzes the NADPH reduction of the resulting 4-keto product. However, in some strains and serotypes of C. jejuni, there are two separate C4-reductases with different product specificities in the gene cluster for CPS formation. Five pairs of these tandem C4-reductases were isolated, and the catalytic properties were ascertained. In four out of five cases, one of the two C4-reductases is able to catalyze the isomerization of C3 and C5 of GDP-6-deoxy-4-keto-d-lyxo-heptose, in addition to the catalysis of the reduction of C4, thus bypassing the requirement for a separate C3/C5-isomerase. In each case, the 3'-end of the gene for the first C4-reductase contains a poly-G tract of 8-10 guanine residues that may be used to control the expression and/or catalytic activity of either C4-reductase. The three-dimensional structure of the C4-reductase from serotype HS:15, which only does a reduction of C4, was determined to 1.45 Å resolution in the presence of NADPH and GDP.
Collapse
Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843 US
| | - Manas K. Ghosh
- Department of Chemistry, Texas A&M University, College Station, TX, 77843 US
| | - Alexander S. Riegert
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843 US
| | - James B. Thoden
- Department of Biochemistry, University of Wisconsin-Madison, Madison WI, 53706 US
| | - Hazel M. Holden
- Department of Biochemistry, University of Wisconsin-Madison, Madison WI, 53706 US
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, TX, 77843 US
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843 US
| |
Collapse
|
15
|
Wang L, Gu J, Zhao W, Wang M, Ng KR, Lyu X, Yang R. Reshaping the Binding Pocket of Cellobiose 2-Epimerase for Improved Substrate Affinity and Isomerization Activity for Enabling Green Synthesis of Lactulose. J Agric Food Chem 2022; 70:15879-15893. [PMID: 36475670 DOI: 10.1021/acs.jafc.2c06980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Enzymatic isomerization of lactose into lactulose via cellobiose 2-epimerase (CE) could provide an eco-friendly route for the industrial production of lactulose, a valuable food prebiotic. However, poor substrate affinity for lactose and preference for epimerization over isomerization hinder this application. Previous studies on CE improvement have focused on random mutagenesis or active site rational design; little is known about the relationship between substrate binding and enzyme efficacy, which was hence the subject of this study. First, residues 372W and 308W were identified as key for disaccharide recognition in CEs based on crystal structure alignment of the N-acetyl-glucosamine 2-epimerase superfamily and site-directed mutation. This binding domain was then reshaped through site saturation mutagenesis, resulting in seven mutants with enhanced isomerization activity. The optimal mutant CsCE/Q371E had significantly enhanced substrate affinity (Km, 269.65 mM vs Km, 417.5 mM), reduced epimerization activity, and 3.3-fold increased isomerization activity over the original CsCE. Molecular dynamics simulation further revealed that substituting Gln-371 with Glu strengthened the hydrogen-bonding network and altered the active site-substrate interactions, increasing the substrate stability and shifting the catalytic direction. This study uncovered new information about the substrate binding region and its mechanisms and impact on CE catalytic performance, paving the way for potential commercial applications.
Collapse
Affiliation(s)
- Lu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jiali Gu
- College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Wei Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingming Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Kuan Rei Ng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
16
|
Zhang W, Wei M, Sun X, Lu F, Guan L, Mao S, Qin HM. Fine-Tuning of Carbon Flux and Artificial Promoters in Bacillus subtilis Enables High-Level Biosynthesis of d-Allulose. J Agric Food Chem 2022; 70:13935-13944. [PMID: 36278912 DOI: 10.1021/acs.jafc.2c05585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
d-Allulose is an attractive rare sugar that can be used as a low-calorie sweetener with significant health benefits. To meet the increasing market demands, it is necessary to develop an efficient and extensive microbial fermentation platform for the synthesis of d-allulose. Here, we applied a comprehensive systematic engineering strategy in Bacillus subtilis WB600 by introducing d-allulose 3-epimerase (DAEase), combined with the deactivation of fruA, levDEFG, and gmuE, to balance the metabolic network for the efficient production of d-allulose. This resulting strain initially produced 3.24 g/L of d-allulose with a yield of 0.93 g of d-allulose/g d-fructose. We further screened and obtained a suitable dual promoter combination and performed fine-tuning of its spacer region. After 64 h of fed-batch fermentation, the optimized engineered B. subtilis produced d-allulose at titers of 74.2 g/L with a yield of 0.93 g/g and a conversion rate of 27.6%. This d-allulose production strain is a promising platform for the industrial production of rare sugar.
Collapse
Affiliation(s)
- Wei Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Meijing Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Xiaoxuan Sun
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Lijun Guan
- Institute of Food Processing, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| |
Collapse
|
17
|
Van Bergen NJ, Walvekar AS, Patraskaki M, Sikora T, Linster CL, Christodoulou J. Clinical and biochemical distinctions for a metabolite repair disorder caused by NAXD or NAXE deficiency. J Inherit Metab Dis 2022; 45:1028-1038. [PMID: 35866541 PMCID: PMC9804276 DOI: 10.1002/jimd.12541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 01/05/2023]
Abstract
The central cofactors NAD(P)H are prone to damage by hydration, resulting in formation of redox-inactive derivatives designated NAD(P)HX. The highly conserved enzymes NAD(P)HX dehydratase (NAXD) and NAD(P)HX epimerase (NAXE) function to repair intracellular NAD(P)HX. Recently, pathogenic variants in both the NAXD and NAXE genes were associated with rapid deterioration and death after an otherwise trivial fever, infection, or illness in young patients. As more patients are identified, distinct clinical features are emerging depending on the location of the pathogenic variant. In this review, we carefully catalogued the clinical features of all published NAXD deficiency patients and found distinct patterns in clinical presentations depending on which subcellular compartment is affected by the enzymatic deficiency. Exon 1 of NAXD contains a mitochondrial propeptide, and a unique cytosolic isoform is initiated from an alternative start codon in exon 2. NAXD deficiency patients with variants that affect both the cytosolic and mitochondrial isoforms present with neurological defects, seizures and skin lesions. Interestingly, patients with NAXD variants exclusively affecting the mitochondrial isoform present with myopathy, moderate neuropathy and a cardiac presentation, without the characteristic skin lesions, seizures or neurological degeneration. This suggests that cytosolic NAD(P)HX repair may protect from neurological damage, whereas muscle fibres may be more sensitive to mitochondrial NAD(P)HX damage. A deeper understanding of the clinical phenotype may facilitate rapid identification of new cases and allow earlier therapeutic intervention. Niacin-based therapies are promising, but advances in disease modelling for both NAXD and NAXE deficiency may identify more specific compounds as targeted treatments. In this review, we found distinct patterns in the clinical presentations of NAXD deficiency patients based on the location of the pathogenic variant, which determines the subcellular compartment that is affected by the enzymatic deficiency.
Collapse
Affiliation(s)
- Nicole J. Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Adhish S. Walvekar
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Myrto Patraskaki
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Tim Sikora
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Carole L. Linster
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgBelvauxLuxembourg
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Victorian Clinical Genetics ServicesRoyal Children's HospitalMelbourneVictoriaAustralia
| |
Collapse
|
18
|
Ghosh MK, Xiang DF, Raushel FM. Product Specificity of C4-Reductases in the Biosynthesis of GDP-6-Deoxy-Heptoses during Capsular Polysaccharide Formation in Campylobacter jejuni. Biochemistry 2022; 61:2138-2147. [PMID: 36107882 PMCID: PMC9623850 DOI: 10.1021/acs.biochem.2c00365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Campylobacter jejuni is the leading cause of food poisoning in the United States and Europe. A capsular polysaccharide that coats the exterior of the bacterium helps evade the host immune system. At least 33 different strains of C. jejuni have been identified, and the chemical structures of 12 different capsular polysaccharides (CPSs) have been characterized from various serotypes. Thus far, 10 different heptose sugars have been found in the chemically characterized CPSs, and each of these are currently thought to originate from the modification of GDP-d-glycero-d-manno-heptose by the successive action of 4,6-dehydratase (or C4-dehydrogenase), C3- or C3/C5-epimerase, and C4-reductase. Within the sequenced strains of C. jejuni, we have identified 25 different C4-reductases that cluster into nine groups at a sequence identity of >90%. Eight of the proteins from seven different clusters were purified, and their product profiles were determined with GDP-6-deoxy-4-keto-heptose substrates using NMR and ESI mass spectrometry. The isolated products included GDP-6-deoxy-l-gluco-heptose (serotype HS:2), GDP-6-deoxy-l-galacto-heptose (serotype HS:42), GDP-6-deoxy-l-gulo-heptose (serotype HS:15), GDP-6-deoxy-d-ido-heptose (serotypes HS:3, HS:4, and HS:33), GDP-6-deoxy-d-manno-heptose (serotype HS:53), and GDP-6-deoxy-d-altro-heptose (serotype HS:23/36). Based on these observations, the product specificity can be reliably predicted for 14 additional C4-reductases from C. jejuni. The remaining three C4-reductases are highly likely to be required for the biosynthesis of 3,6-dideoxy-heptose products.
Collapse
Affiliation(s)
- Manas K. Ghosh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dao Feng Xiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
19
|
Liu Z, Wang Y, Liu S, Guo X, Zhao T, Wu J, Chen S. Boosting the Heterologous Expression of d-Allulose 3-Epimerase in Bacillus subtilis through Protein Engineering and Catabolite-Responsive Element Box Engineering. J Agric Food Chem 2022; 70:12128-12134. [PMID: 36099523 DOI: 10.1021/acs.jafc.2c04800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As a natural sweetener with low calories and various physiological activities, d-allulose has drawn worldwide attention. Currently, d-allulose 3-epimerase (DAEase) is mainly used to catalyze the epimerization of d-fructose to d-allulose. Therefore, it is quite necessary to enhance the food-grade expression of DAEase to meet the surging market demand for d-allulose. In this study, initially, the promising variant H207L/D281G/C289R of Clostridium cellulolyticum H10 DAEase (CcDAEase) was generated by protein engineering, the specific activity and the T1/2 of which were 2.24-fold and 13.45-fold those of the CcDAEase wild type at 60 °C, respectively. After that, PamyE was determined as the optimal promoter for the recombinant expression of CcDAEase in Bacillus subtilis, and catabolite-responsive element (CRE) box engineering was further performed to eliminate the carbon catabolite repression (CCR) effect. Lastly, high-density fermentation was carried out and the final activity peaked at 4971.5 U mL-1, which is the highest expression level and could effectively promote the industrial production of DAEase. This research provides a theoretical basis and technical support for the molecular modification of DAEase and its efficient fermentation preparation.
Collapse
Affiliation(s)
- Zhanzhi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Yifan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Shuhan Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Xuehong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Tianlong Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| |
Collapse
|
20
|
Ghosh MK, Xiang DF, Thoden JB, Holden HM, Raushel FM. C3- and C3/C5-Epimerases Required for the Biosynthesis of the Capsular Polysaccharides from Campylobacter jejuni. Biochemistry 2022; 61:2036-2048. [PMID: 36093987 PMCID: PMC9631236 DOI: 10.1021/acs.biochem.2c00364] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Campylobacter jejuni is a human pathogen and one of the leading causes of food poisoning in Europe and the United States. The outside of the bacterium is coated with a capsular polysaccharide that assists in the evasion of the host immune system. Many of the serotyped strains of C. jejuni contain a 6-deoxy-heptose moiety that is biosynthesized from GDP-d-glycero-d-manno-heptose by the successive actions of a 4,6-dehydratase, a C3/C5-epimerase, and a C4-reductase. We identified 18 different C3/C5-epimerases that could be clustered together into three groups at a sequence identity of >89%. Four of the enzymes from the largest cluster (from serotypes HS:3, HS:10, HS:23/36, and HS:41) were shown to only catalyze the epimerization at C3. Three enzymes from the second largest cluster (HS:2, HS:15, and HS:42) were shown to catalyze the epimerization at C3 and C5. Enzymes from the third cluster were not characterized. The three-dimensional structures of the epimerases from serotypes HS:3, HS:23/36, HS:15, and HS:41 were determined to resolutions of 1.5-1.9 Å. The overall subunit architecture places these enzymes into the diverse "cupin" superfamily. Within X-ray coordinate error, the immediate regions surrounding the active sites are identical, suggesting that factors extending farther out may influence product outcome. The X-ray crystal structures are consistent with His-67 and Tyr-134 acting as general acid/base catalysts for the epimerization of C3 and/or C5. Two amino acid changes (A76V/C136L) were enough to convert the C3-epimerase from serotype HS:3 to one that could now catalyze the epimerization at both C3 and C5.
Collapse
Affiliation(s)
- Manas K. Ghosh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dao Feng Xiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - James B. Thoden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Hazel M. Holden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Frank M. Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
21
|
Nygaard RH, Nielsen MC, Antonsen KW, Højskov CS, Sørensen BS, Møller HJ. Metabolism of 25-Hydroxy-Vitamin D in Human Macrophages Is Highly Dependent on Macrophage Polarization. Int J Mol Sci 2022; 23:ijms231810943. [PMID: 36142855 PMCID: PMC9505540 DOI: 10.3390/ijms231810943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Macrophages synthesize active vitamin D (1,25-dihydroxy-vitamin D) and express the vitamin D receptor in the nucleus; however, vitamin D metabolism in relation to macrophage polarization and function is not well understood. We studied monocyte-derived macrophages (MDMs) from human buffy coats polarized into M0, M1 (LPS + IFNγ), M2a (IL4 + IL13) and M2c (IL10) macrophage subtypes stimulated with 25-hydroxy-vitamin D (1000 and 10,000 nanomolar). We measured vitamin D metabolites (25-hydroxy-vitamin D, 1,25-dihydroxy-vitamin D, 24,25-dihydroxy-vitamin D and 3-epi-25-hydroxy-vitamin D) in cell media with liquid chromatography-mass spectrometry-mass spectrometry. The mRNA expression (CYP27B1, CYP24A1 and CYP24A1-SV) was measured with qPCR. We found that reparative MDMs (M2a) had significantly more 1,25-dihydroxy-vitamin D compared to the other MDMs (M0, M1 and M2c). All MDMs were able to produce 3-epi-25-hydroxy-vitamin D, but this pathway was almost completely attenuated in inflammatory M1 MDMs. All MDM subtypes degraded vitamin D through the 24-hydroxylase pathway, although M1 MDMs mainly expressed an inactive splice variant of CYP24A1, coding the degrading enzyme. In conclusion, this study shows that vitamin D metabolism is highly dependent on macrophage polarization and that the C3-epimerase pathway for vitamin D is active in macrophages.
Collapse
Affiliation(s)
- Rie H. Nygaard
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
- Correspondence: ; Tel.: +45-4046-5768
| | - Marlene C. Nielsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Kristian W. Antonsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Carsten S. Højskov
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Boe S. Sørensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark
| | - Holger J. Møller
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark
| |
Collapse
|
22
|
Xia N, Guo X, Guo Q, Gupta N, Ji N, Shen B, Xiao L, Feng Y. Metabolic flexibilities and vulnerabilities in the pentose phosphate pathway of the zoonotic pathogen Toxoplasma gondii. PLoS Pathog 2022; 18:e1010864. [PMID: 36121870 PMCID: PMC9521846 DOI: 10.1371/journal.ppat.1010864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/29/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Metabolic pathways underpin the growth and virulence of intracellular parasites and are therefore promising antiparasitic targets. The pentose phosphate pathway (PPP) is vital in most organisms, providing a reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) and ribose sugar for nucleotide synthesis; however, it has not yet been studied in Toxoplasma gondii, a widespread intracellular pathogen and a model protozoan organism. Herein, we show that T. gondii has a functional PPP distributed in the cytoplasm and nucleus of its acutely-infectious tachyzoite stage. We produced eight parasite mutants disrupting seven enzymes of the PPP in T. gondii. Our data show that of the seven PPP proteins, the two glucose-6-phosphate dehydrogenases (TgG6PDH1, TgG6PDH2), one of the two 6-phosphogluconate dehydrogenases (Tg6PGDH1), ribulose-5-phosphate epimerase (TgRuPE) and transaldolase (TgTAL) are dispensable in vitro as well as in vivo, disclosing substantial metabolic plasticity in T. gondii. Among these, TgG6PDH2 plays a vital role in defense against oxidative stress by the pathogen. Further, we show that Tg6PGDH2 and ribulose-5-phosphate isomerase (TgRPI) are critical for tachyzoite growth. The depletion of TgRPI impairs the flux of glucose in central carbon pathways, and causes decreased expression of ribosomal, microneme and rhoptry proteins. In summary, our results demonstrate the physiological need of the PPP in T. gondii while unraveling metabolic flexibility and antiparasitic targets. Metabolic pathways are intimately associated with the survival and replication of parasitic Toxoplasma gondii and thus represent potential targets for antiparasitic strategies. Herein, we focused on the pentose phosphate pathway (PPP) in T. gondii and examined its roles in supporting the growth of this ubiquitous pathogen. We found that TgG6PDH1 and TgG6PDH2 were needed to defend oxidative stress but not for pentose synthesis. We revealed that inactivation of the Tg6PGDH2 and TgRPI severely impaired the asexual reproduction of tachyzoites. We also highlighted the remarkable metabolic plasticity in tachyzoites that enables them to acquire some of the PPP intermediates from multiple routes. This study provides significant insights into the carbon metabolism properties of Toxoplasma parasites, opening avenues for targeting this pathway to develop therapeutic interventions against toxoplasmosis.
Collapse
Affiliation(s)
- Ningbo Xia
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuefang Guo
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qinghong Guo
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Nishith Gupta
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (Hyderabad Campus), Hyderabad, India
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Nuo Ji
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bang Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- * E-mail: (BS); (LX); (YF)
| | - Lihua Xiao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- * E-mail: (BS); (LX); (YF)
| | - Yaoyu Feng
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- * E-mail: (BS); (LX); (YF)
| |
Collapse
|
23
|
Sang L, Chen G, Cao J, Liu J, Yu Y. PhRHMs play important roles in leaf and flower development and anthocyanin synthesis in petunia. Physiol Plant 2022; 174:e13773. [PMID: 36066309 DOI: 10.1111/ppl.13773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Anthocyanins, vital metabolites in plants, are formed by anthocyanidins combined with various monosaccharides, including glucose, rhamnose, and arabinose. Rhamnose contributes greatly to the glycosylation of anthocyanidins. There are two kinds of rhamnose synthase (RS): rhamnose biosynthesis (RHM), and nucleotide-RS/epimerase-reductase (UER1). Nevertheless, no RS isoform was reported to be involved in anthocyanin synthesis. Here, three homologous PhRHM genes, namely PhRHM1, PhRHM2, and PhRHM3, and one PhUER1 gene from petunia were cloned and characterized. Green fluorescent protein fusion protein assays revealed that PhRHMs and PhUER1 are localized in the cytoplasm. We obtained PhRHM1 or/and PhRHM2 or PhUER1 silenced petunia plants and did not attempt to obtain PhRHM3 silenced plants since PhRHM3 mRNA was not detected in petunia organs examined. PhRHM1 and PhRHM2 (PhRHM1-2) silencing induced abnormal plant growth and decreased the contents of l-rhamnose, photosynthetic pigments and total anthocyanins, while PhUER1 silencing did not cause any visible phenotypic changes. Flavonoid metabolome analysis further revealed that PhRHM1-2 silencing reduced the contents of anthocyanins with rhamnose residue. These results revealed that PhRHMs contribute to the biosynthesis of rhamnose and that PhRHMs participate in the anthocyanin rhamnosylation in petunia, while PhUER1 does not.
Collapse
Affiliation(s)
- Lina Sang
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guoju Chen
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiahao Cao
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yixun Yu
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| |
Collapse
|
24
|
Li S, Chen F, Li Y, Wang L, Li H, Gu G, Li E. Rhamnose-Containing Compounds: Biosynthesis and Applications. Molecules 2022; 27:molecules27165315. [PMID: 36014553 PMCID: PMC9415975 DOI: 10.3390/molecules27165315] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Rhamnose-associated molecules are attracting attention because they are present in bacteria but not mammals, making them potentially useful as antibacterial agents. Additionally, they are also valuable for tumor immunotherapy. Thus, studies on the functions and biosynthetic pathways of rhamnose-containing compounds are in progress. In this paper, studies on the biosynthetic pathways of three rhamnose donors, i.e., deoxythymidinediphosphate-L-rhamnose (dTDP-Rha), uridine diphosphate-rhamnose (UDP-Rha), and guanosine diphosphate rhamnose (GDP-Rha), are firstly reviewed, together with the functions and crystal structures of those associated enzymes. Among them, dTDP-Rha is the most common rhamnose donor, and four enzymes, including glucose-1-phosphate thymidylyltransferase RmlA, dTDP-Glc-4,6-dehydratase RmlB, dTDP-4-keto-6-deoxy-Glc-3,5-epimerase RmlC, and dTDP-4-keto-Rha reductase RmlD, are involved in its biosynthesis. Secondly, several known rhamnosyltransferases from Geobacillus stearothermophilus, Saccharopolyspora spinosa, Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Streptococcus pneumoniae are discussed. In these studies, however, the functions of rhamnosyltransferases were verified by employing gene knockout and radiolabeled substrates, which were almost impossible to obtain and characterize the products of enzymatic reactions. Finally, the application of rhamnose-containing compounds in disease treatments is briefly described.
Collapse
Affiliation(s)
- Siqiang Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Fujia Chen
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Yun Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Lizhen Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, China
| | - Hongyan Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
| | - Guofeng Gu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
- Correspondence: (G.G.); (E.L.)
| | - Enzhong Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
- Correspondence: (G.G.); (E.L.)
| |
Collapse
|
25
|
Manor J, Calame D, Gijavanekar C, Fisher K, Hunter J, Mizerik E, Bacino C, Scaglia F, Elsea SH. NAXE deficiency: A neurometabolic disorder of NAD(P)HX repair amenable for metabolic correction. Mol Genet Metab 2022; 136:101-110. [PMID: 35637064 PMCID: PMC9893913 DOI: 10.1016/j.ymgme.2022.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023]
Abstract
The NAD(P)HX repair system is a metabolite damage repair mechanism responsible for restoration of NADH and NADPH after their inactivation by hydration. Deficiency in either of its two enzymes, NAD(P)HX dehydratase (NAXD) or NAD(P)HX epimerase (NAXE), causes a fatal neurometabolic disorder characterized by decompensations precipitated by inflammatory stress. Clinical findings include rapidly progressive muscle weakness, ataxia, ophthalmoplegia, and motor and cognitive regression, while neuroimaging abnormalities are subtle or nonspecific, making a clinical diagnosis challenging. During stress, nonenzymatic conversion of NAD(P)H to NAD(P)HX increases, and in the absence of repair, NAD(P)H is depleted, and NAD(P)HX accumulates, leading to decompensation; however, the contribution of each to the metabolic derangement is not established. Herein, we summarize the clinical knowledge of NAXE deficiency from 30 cases and lessons learned about disease pathogenesis from cell cultures and model organisms and describe a metabolomics signature obtained by untargeted metabolomics analysis in one case at the time of crisis and after initiation of treatment. Overall, biochemical findings support a model of acute depletion of NAD+, signs of mitochondrial dysfunction, and altered lipidomics. These findings are further substantiated by untargeted metabolomics six months post-crisis showing that niacin supplementation reverses primary metabolomic abnormalities concurrent with improved clinical status.
Collapse
Affiliation(s)
- Joshua Manor
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Metabolic Diseases Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Israel.
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Charul Gijavanekar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kristen Fisher
- Texas Children's Hospital, Houston, TX, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jill Hunter
- Texas Children's Hospital, Houston, TX, USA; Department of Radiology, Texas Children's Hospital, Houston, TX, USA
| | - Elizabeth Mizerik
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Carlos Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, Sha Tin, Hong Kong
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
26
|
Duan M, Chen H, Yin L, Zhu X, Novák P, Lv Y, Zhao G, Yin K. Mitochondrial apolipoprotein A-I binding protein alleviates atherosclerosis by regulating mitophagy and macrophage polarization. Cell Commun Signal 2022; 20:60. [PMID: 35525979 PMCID: PMC9077873 DOI: 10.1186/s12964-022-00858-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/05/2022] [Indexed: 12/22/2022] Open
Abstract
Apolipoprotein A-I binding protein (AIBP), a secreted protein, has been shown to play a pivotal role in the development of atherosclerosis. The function of intracellular AIBP, however, is not yet well characterized. Here, we found that AIBP is abundantly expressed within human and mouse atherosclerotic lesions and exhibits a distinct localization in the inner membrane of mitochondria in macrophages. Bone marrow-specific AIBP deficiency promotes the progression of atherosclerosis and increases macrophage infiltration and inflammation in low-density lipoprotein receptor-deficient (LDLR-/-) mice. Specifically, the lack of mitochondrial AIBP leads to mitochondrial metabolic disorders, thereby reducing the formation of mitophagy by promoting the cleavage of PTEN-induced putative kinase 1 (PINK1). With the reduction in mitochondrial autophagy, macrophages polarize to the M1 proinflammatory phenotype, which further promotes the development of atherosclerosis. Based on these results, mitochondrial AIBP in macrophages performs an antiatherosclerotic role by regulating of PINK1-dependent mitophagy and M1/M2 polarization. Video Abstract.
Collapse
Affiliation(s)
- Meng Duan
- Department of Cardiology, The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, 541100 Guangxi China
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin, Guangxi China
- Research Lab of Translational Medicine, Hengyang Medical School, University of South China, Hengyang, China
| | - Hainan Chen
- Research Lab of Translational Medicine, Hengyang Medical School, University of South China, Hengyang, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Linjie Yin
- Research Lab of Translational Medicine, Hengyang Medical School, University of South China, Hengyang, China
| | - Xiao Zhu
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin, Guangxi China
| | - Petr Novák
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin, Guangxi China
| | - Yuncheng Lv
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin, Guangxi China
| | - Guojun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan City People’s Hospital, Qingyuan, 511518 Guangdong China
| | - Kai Yin
- Department of Cardiology, The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, 541100 Guangxi China
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin, Guangxi China
- Research Lab of Translational Medicine, Hengyang Medical School, University of South China, Hengyang, China
| |
Collapse
|
27
|
Liangfei L, Yafeng Z, Kai X, Zheng X. Identification of a thermostable cellobiose 2-epimerase from Caldicellulosiruptor sp. Rt8.B8 and production of epilactose using Bacillus subtilis. J Sci Food Agric 2022; 102:85-94. [PMID: 34031874 DOI: 10.1002/jsfa.11333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 05/17/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Epilactose, a potential prebiotics, was derived from lactose through enzymatic catalysis. However, production and purification of epilactose are currently difficult due to powerless enzymes and inefficient downstream processing steps. RESULTS The encoding gene of cellobiose 2-epimerase (CE) from Caldicellulosiruptor sp. Rt8.B8 was cloned and expressed in Escherichia coli BL21(DE3). The enzyme was purified and it was suitable for industrial production of epilactose from lactose without by-products, because of high kcat (197.6 s-1 ) and preferable thermostability. The Rt8-CE gene was further expressed in the Bacillus subtilis strain. We successfully produced epilactose from 700 g L-1 lactose in 30.4% yield by using the recombinant Bacillus subtilis whole cells. By screening of a β-galactosidase from Bacillus stearothermophilus (BsGal), a process for separating epilactose and lactose was established, which showed a purity of over 95% in a total yield of 69.2%. In addition, a mixed rare sugar syrup composed of epilactose and d-tagatose was successfully produced from lactose through the co-expression of l-arabinose isomerase and β-galactosidase. CONCLUSION Our study shed light on the efficient production of epilactose using a food-grade host expressing a novel CE enzyme. Moreover, an efficient and low-cost process was attempted to obtain high purity epilactose. In order to improve the utilization of raw materials, the production process of mixed syrup containing epilactose and d-tagatose with prebiotic properties produced from lactose was also established for the first time. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Li Liangfei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhu Yafeng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xu Kai
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Xu Zheng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| |
Collapse
|
28
|
Lloyd MD, Yevglevskis M, Nathubhai A, James TD, Threadgill MD, Woodman TJ. Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition. Chem Soc Rev 2021; 50:5952-5984. [PMID: 34027955 PMCID: PMC8142540 DOI: 10.1039/d0cs00540a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Racemases and epimerases catalyse changes in the stereochemical configurations of chiral centres and are of interest as model enzymes and as biotechnological tools. They also occupy pivotal positions within metabolic pathways and, hence, many of them are important drug targets. This review summarises the catalytic mechanisms of PLP-dependent, enolase family and cofactor-independent racemases and epimerases operating by a deprotonation/reprotonation (1,1-proton transfer) mechanism and methods for measuring their catalytic activity. Strategies for inhibiting these enzymes are reviewed, as are specific examples of inhibitors. Rational design of inhibitors based on substrates has been extensively explored but there is considerable scope for development of transition-state mimics and covalent inhibitors and for the identification of inhibitors by high-throughput, fragment and virtual screening approaches. The increasing availability of enzyme structures obtained using X-ray crystallography will facilitate development of inhibitors by rational design and fragment screening, whilst protein models will facilitate development of transition-state mimics.
Collapse
Affiliation(s)
- Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and CatSci Ltd., CBTC2, Capital Business Park, Wentloog, Cardiff CF3 2PX, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and University of Sunderland, School of Pharmacy & Pharmaceutical Sciences, Sciences Complex, Sunderland SR1 3SD, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK and School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, People's Republic of China
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3BY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| |
Collapse
|
29
|
Kim JD, Zhu L, Sun Q, Fang L. Systemic metabolite profiling reveals sexual dimorphism of AIBP control of metabolism in mice. PLoS One 2021; 16:e0248964. [PMID: 33793635 PMCID: PMC8016339 DOI: 10.1371/journal.pone.0248964] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/08/2021] [Indexed: 01/04/2023] Open
Abstract
Emerging studies indicate that APOA-I binding protein (AIBP) is a secreted protein and functions extracellularly to promote cellular cholesterol efflux, thereby disrupting lipid rafts on the plasma membrane. AIBP is also present in the mitochondria and acts as an epimerase, facilitating the repair of dysfunctional hydrated NAD(P)H, known as NAD(P)H(X). Importantly, AIBP deficiency contributes to lethal neurometabolic disorder, reminiscent of the Leigh syndrome in humans. Whereas cyclic NADPHX production is proposed to be the underlying cause, we hypothesize that an unbiased metabolic profiling may: 1) reveal new clues for the lethality, e.g., changes of mitochondrial metabolites., and 2) identify metabolites associated with new AIBP functions. To this end, we performed unbiased and profound metabolic studies of plasma obtained from adult AIBP knockout mice and control littermates of both genders. Our systemic metabolite profiling, encompassing 9 super pathways, identified a total of 640 compounds. Our studies demonstrate a surprising sexual dimorphism of metabolites affected by AIBP deletion, with more statistically significant changes in the AIBP knockout female vs male when compared with the corresponding controls. AIBP knockout trends to reduce cholesterol but increase the bile acid precursor 7-HOCA in female but not male. Complex lipids, phospholipids, sphingomyelin and plasmalogens were reduced, while monoacylglycerol, fatty acids and the lipid soluble vitamins E and carotene diol were elevated in AIBP knockout female but not male. NAD metabolites were not significantly different in AIBP knockout vs control mice but differed for male vs female mice. Metabolites associated with glycolysis and the Krebs cycle were unchanged by AIBP knockout. Importantly, polyamine spermidine, critical for many cellular functions including cerebral cortex synapses, was reduced in male but not female AIBP knockout. This is the first report of a systemic metabolite profile of plasma samples from AIBP knockout mice, and provides a metabolic basis for future studies of AIBP regulation of cellular metabolism and the pathophysiological presentation of AIBP deficiency in patients.
Collapse
Affiliation(s)
- Jun-dae Kim
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, United States of America
| | - Lingping Zhu
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, United States of America
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Quan Sun
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, United States of America
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Longhou Fang
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, United States of America
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States of America
- Weill Cornell Medical College, New York, NY, United States of America
- * E-mail:
| |
Collapse
|
30
|
Choi SH, Agatisa-Boyle C, Gonen A, Kim A, Kim J, Alekseeva E, Tsimikas S, Miller YI. Intracellular AIBP (Apolipoprotein A-I Binding Protein) Regulates Oxidized LDL (Low-Density Lipoprotein)-Induced Mitophagy in Macrophages. Arterioscler Thromb Vasc Biol 2021; 41:e82-e96. [PMID: 33356389 PMCID: PMC8105271 DOI: 10.1161/atvbaha.120.315485] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Atherosclerotic lesions are often characterized by accumulation of OxLDL (oxidized low-density lipoprotein), which is associated with vascular inflammation and lesion vulnerability to rupture. Extracellular AIBP (apolipoprotein A-I binding protein; encoded by APOA1BP gene), when secreted, promotes cholesterol efflux and regulates lipid rafts dynamics, but its role as an intracellular protein in mammalian cells remains unknown. The aim of this work was to determine the function of intracellular AIBP in macrophages exposed to OxLDL and in atherosclerotic lesions. Approach and Results: Using a novel monoclonal antibody against human and mouse AIBP, which are highly homologous, we demonstrated robust AIBP expression in human and mouse atherosclerotic lesions. We observed significantly reduced autophagy in bone marrow-derived macrophages, isolated from Apoa1bp-/- compared with wild-type mice, which were exposed to OxLDL. In atherosclerotic lesions from Apoa1bp-/- mice subjected to Ldlr knockdown and fed a Western diet, autophagy was reduced, whereas apoptosis was increased, when compared with that in wild-type mice. AIBP expression was necessary for efficient control of reactive oxygen species and cell death and for mitochondria quality control in macrophages exposed to OxLDL. Mitochondria-localized AIBP, via its N-terminal domain, associated with E3 ubiquitin-protein ligase PARK2 (Parkin), MFN (mitofusin)1, and MFN2, but not BNIP3 (Bcl2/adenovirus E1B 19-kDa-interacting protein-3), and regulated ubiquitination of MFN1 and MFN2, key components of mitophagy. CONCLUSIONS These data suggest that intracellular AIBP is a new regulator of autophagy in macrophages. Mitochondria-localized AIBP augments mitophagy and participates in mitochondria quality control, protecting macrophages against cell death in the context of atherosclerosis.
Collapse
Affiliation(s)
- Soo-Ho Choi
- Department of Medicine University of California San Diego, La Jolla, CA 92093
| | - Colin Agatisa-Boyle
- Department of Medicine University of California San Diego, La Jolla, CA 92093
| | - Ayelet Gonen
- Department of Medicine University of California San Diego, La Jolla, CA 92093
| | - Alisa Kim
- Department of Medicine University of California San Diego, La Jolla, CA 92093
| | - Jungsu Kim
- Department of Medicine University of California San Diego, La Jolla, CA 92093
| | - Elena Alekseeva
- Department of Medicine University of California San Diego, La Jolla, CA 92093
| | - Sotirios Tsimikas
- Department of Medicine University of California San Diego, La Jolla, CA 92093
| | - Yury I. Miller
- Department of Medicine University of California San Diego, La Jolla, CA 92093
| |
Collapse
|
31
|
Barnawi H, Woodward L, Fava N, Roubakha M, Shaw SD, Kubinec C, Naismith JH, Creuzenet C. Structure-function studies of the C3/C5 epimerases and C4 reductases of the Campylobacter jejuni capsular heptose modification pathways. J Biol Chem 2021; 296:100352. [PMID: 33524389 PMCID: PMC7949155 DOI: 10.1016/j.jbc.2021.100352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/14/2023] Open
Abstract
Many bacteria produce polysaccharide-based capsules that protect them from environmental insults and play a role in virulence, host invasion, and other functions. Understanding how the polysaccharide components are synthesized could provide new means to combat bacterial infections. We have previously characterized two pairs of homologous enzymes involved in the biosynthesis of capsular sugar precursors GDP-6-deoxy-D-altro-heptose and GDP-6-OMe-L-gluco-heptose in Campylobacter jejuni. However, the substrate specificity and mechanism of action of these enzymes-C3 and/or C5 epimerases DdahB and MlghB and C4 reductases DdahC and MlghC-are unknown. Here, we demonstrate that these enzymes are highly specific for heptose substrates, using mannose substrates inefficiently with the exception of MlghB. We show that DdahB and MlghB feature a jellyroll fold typical of cupins, which possess a range of activities including epimerizations, GDP occupying a similar position as in cupins. DdahC and MlghC contain a Rossman fold, a catalytic triad, and a small C-terminal domain typical of short-chain dehydratase reductase enzymes. Integrating structural information with site-directed mutagenesis allowed us to identify features unique to each enzyme and provide mechanistic insight. In the epimerases, mutagenesis of H67, D173, N121, Y134, and Y132 suggested the presence of alternative catalytic residues. We showed that the reductases could reduce GDP-4-keto-6-deoxy-mannulose without prior epimerization although DdahC preferred the pre-epimerized substrate and identified T110 and H180 as important for substrate specificity and catalytic efficacy. This information can be exploited to identify inhibitors for therapeutic applications or to tailor these enzymes to synthesize novel sugars useful as glycobiology tools.
Collapse
Affiliation(s)
- Heba Barnawi
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Laura Woodward
- Biomedical Sciences Research Complex, St Andrews University, St Andrews, UK
| | - Natalie Fava
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Mikhail Roubakha
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Steve D Shaw
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Chelsea Kubinec
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - James H Naismith
- Biomedical Sciences Research Complex, St Andrews University, St Andrews, UK; Rosalind Franklin Institute, Research Complex at Harwell, Harwell Campus, Didcot, UK; Division of Structural Biology, Oxford University, Oxford, UK.
| | - Carole Creuzenet
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada.
| |
Collapse
|
32
|
Ploux E, Bouet V, Radzishevsky I, Wolosker H, Freret T, Billard JM. Serine Racemase Deletion Affects the Excitatory/Inhibitory Balance of the Hippocampal CA1 Network. Int J Mol Sci 2020; 21:E9447. [PMID: 33322577 PMCID: PMC7763099 DOI: 10.3390/ijms21249447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
d-serine is the major co-agonist of N-methyl-D-aspartate receptors (NMDAR) at CA3/CA1 hippocampal synapses, the activation of which drives long-term potentiation (LTP). The use of mice with targeted deletion of the serine racemase (SR) enzyme has been an important tool to uncover the physiological and pathological roles of D-serine. To date, some uncertainties remain regarding the direction of LTP changes in SR-knockout (SR-KO) mice, possibly reflecting differences in inhibitory GABAergic tone in the experimental paradigms used in the different studies. On the one hand, our extracellular recordings in hippocampal slices show that neither isolated NMDAR synaptic potentials nor LTP were altered in SR-KO mice. This was associated with a compensatory increase in hippocampal levels of glycine, another physiologic NMDAR co-agonist. SR-KO mice displayed no deficits in spatial learning, reference memory and cognitive flexibility. On the other hand, SR-KO mice showed a weaker LTP and a lower increase in NMDAR potentials compared to controls when GABAA receptors were pharmacologically blocked. Our results indicate that depletion of endogenous D-serine caused a reduced inhibitory activity in CA1 hippocampal networks, altering the excitatory/inhibitory balance, which contributes to preserve functional plasticity at synapses and to maintain related cognitive abilities.
Collapse
Affiliation(s)
- Eva Ploux
- UNICAEN, INSERM, COMETE, Cyceron, CHU Caen, Normandie University, 14000 Caen, France; (E.P.); (V.B.); (T.F.)
| | - Valentine Bouet
- UNICAEN, INSERM, COMETE, Cyceron, CHU Caen, Normandie University, 14000 Caen, France; (E.P.); (V.B.); (T.F.)
| | - Inna Radzishevsky
- Department of Biochemistry, Technion-Israel Institute of Technology, Rappaport Faculty of Medicine, Haifa 31096, Israel; (I.R.); (H.W.)
| | - Herman Wolosker
- Department of Biochemistry, Technion-Israel Institute of Technology, Rappaport Faculty of Medicine, Haifa 31096, Israel; (I.R.); (H.W.)
| | - Thomas Freret
- UNICAEN, INSERM, COMETE, Cyceron, CHU Caen, Normandie University, 14000 Caen, France; (E.P.); (V.B.); (T.F.)
| | - Jean-Marie Billard
- UNICAEN, INSERM, COMETE, Cyceron, CHU Caen, Normandie University, 14000 Caen, France; (E.P.); (V.B.); (T.F.)
| |
Collapse
|
33
|
Fushinobu S. Molecular evolution and functional divergence of UDP-hexose 4-epimerases. Curr Opin Chem Biol 2020; 61:53-62. [PMID: 33171387 DOI: 10.1016/j.cbpa.2020.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/08/2023]
Abstract
UDP-glucose 4-epimerase (GalE) catalyzes the interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal) and/or the interconversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylgalactosamine (UDP-GalNAc) in sugar metabolism. GalEs belong to the short-chain dehydrogenase/reductase superfamily, use a conserved 'transient keto intermediate' mechanism and have variable substrate specificity. GalEs have been classified into three groups based on substrate specificity: group 1 prefers UDP-Glc/Gal, group 3 prefers UDP-GlcNAc/GalNAc, and group 2 has comparable activities for both types of the substrates. The phylogenetic relationship and structural basis for the specificities of GalEs revealed possible molecular evolution of UDP-hexose 4-epimerases in various organisms. Based on the recent advances in studies on GalEs and related enzymes, an updated view of their evolutional diversification is presented.
Collapse
Affiliation(s)
- Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
| |
Collapse
|
34
|
Abstract
Protein domains exist by themselves or in combination with other domains to form complex multidomain proteins. Defining domain boundaries in proteins is essential for understanding their evolution and function but is not trivial. More specifically, partitioning domains that interact by forming a single β-sheet is known to be particularly troublesome for automatic structure-based domain decomposition pipelines. Here, we study edge-to-edge β-strand interactions between domains in a protein chain, to help define the boundaries for some more difficult cases where a single β-sheet spanning over two domains gives an appearance of one. We give a number of examples where β-strands belonging to a single β-sheet do not belong to a single domain and highlight the difficulties of automatic domain parsers on these examples. This work can be used as a baseline for defining domain boundaries in homologous proteins or proteins with similar domain interactions in the future.
Collapse
Affiliation(s)
- Archana S. Bhat
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
| |
Collapse
|
35
|
Debets MF, Tastan OY, Wisnovsky SP, Malaker SA, Angelis N, Moeckl LKR, Choi J, Flynn H, Wagner LJS, Bineva-Todd G, Antonopoulos A, Cioce A, Browne WM, Li Z, Briggs DC, Douglas HL, Hess GT, Agbay AJ, Roustan C, Kjaer S, Haslam SM, Snijders AP, Bassik MC, Moerner WE, Li VSW, Bertozzi CR, Schumann B. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proc Natl Acad Sci U S A 2020; 117:25293-25301. [PMID: 32989128 DOI: 10.1101/2020.04.23.057208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Protein glycosylation events that happen early in the secretory pathway are often dysregulated during tumorigenesis. These events can be probed, in principle, by monosaccharides with bioorthogonal tags that would ideally be specific for distinct glycan subtypes. However, metabolic interconversion into other monosaccharides drastically reduces such specificity in the living cell. Here, we use a structure-based design process to develop the monosaccharide probe N-(S)-azidopropionylgalactosamine (GalNAzMe) that is specific for cancer-relevant Ser/Thr(O)-linked N-acetylgalactosamine (GalNAc) glycosylation. By virtue of a branched N-acylamide side chain, GalNAzMe is not interconverted by epimerization to the corresponding N-acetylglucosamine analog by the epimerase N-acetylgalactosamine-4-epimerase (GALE) like conventional GalNAc-based probes. GalNAzMe enters O-GalNAc glycosylation but does not enter other major cell surface glycan types including Asn(N)-linked glycans. We transfect cells with the engineered pyrophosphorylase mut-AGX1 to biosynthesize the nucleotide-sugar donor uridine diphosphate (UDP)-GalNAzMe from a sugar-1-phosphate precursor. Tagged with a bioorthogonal azide group, GalNAzMe serves as an O-glycan-specific reporter in superresolution microscopy, chemical glycoproteomics, a genome-wide CRISPR-knockout (CRISPR-KO) screen, and imaging of intestinal organoids. Additional ectopic expression of an engineered glycosyltransferase, "bump-and-hole" (BH)-GalNAc-T2, boosts labeling in a programmable fashion by increasing incorporation of GalNAzMe into the cell surface glycoproteome. Alleviating the need for GALE-KO cells in metabolic labeling experiments, GalNAzMe is a precision tool that allows a detailed view into the biology of a major type of cancer-relevant protein glycosylation.
Collapse
Affiliation(s)
- Marjoke F Debets
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Omur Y Tastan
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nikolaos Angelis
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Junwon Choi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Helen Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lauren J S Wagner
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ganka Bineva-Todd
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Peptide Chemistry Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Anna Cioce
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - William M Browne
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Zhen Li
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - David C Briggs
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Holly L Douglas
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, CA 94305
- Program in Cancer Biology, Stanford University, Stanford, CA 94305
| | - Anthony J Agbay
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjaer
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Stuart M Haslam
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305
- Program in Cancer Biology, Stanford University, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| | - Benjamin Schumann
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom;
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| |
Collapse
|
36
|
Elizondo G, Matern D, Vockley J, Harding CO, Gillingham MB. Effects of fasting, feeding and exercise on plasma acylcarnitines among subjects with CPT2D, VLCADD and LCHADD/TFPD. Mol Genet Metab 2020; 131:90-97. [PMID: 32928639 PMCID: PMC8048763 DOI: 10.1016/j.ymgme.2020.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND The plasma acylcarnitine profile is frequently used as a biochemical assessment for follow-up in diagnosed patients with fatty acid oxidation disorders (FAODs). Disease specific acylcarnitine species are elevated during metabolic decompensation but there is clinical and biochemical heterogeneity among patients and limited data on the utility of an acylcarnitine profile for routine clinical monitoring. METHODS We evaluated plasma acylcarnitine profiles from 30 diagnosed patients with long-chain FAODs (carnitine palmitoyltransferase-2 (CPT2), very long-chain acyl-CoA dehydrogenase (VLCAD), and long-chain 3-hydroxy acyl-CoA dehydrogenase or mitochondrial trifunctional protein (LCHAD/TFP) deficiencies) collected after an overnight fast, after feeding a controlled low-fat diet, and before and after moderate exercise. Our purpose was to describe the variability in this biomarker and how various physiologic states effect the acylcarnitine concentrations in circulation. RESULTS Disease specific acylcarnitine species were higher after an overnight fast and decreased by approximately 60% two hours after a controlled breakfast meal. Moderate-intensity exercise increased the acylcarnitine species but it varied by diagnosis. When analyzed for a genotype/phenotype correlation, the presence of the common LCHADD mutation (c.1528G > C) was associated with higher levels of 3-hydroxyacylcarnitines than in patients with other mutations. CONCLUSIONS We found that feeding consistently suppressed and that moderate intensity exercise increased disease specific acylcarnitine species, but the response to exercise was highly variable across subjects and diagnoses. The clinical utility of routine plasma acylcarnitine analysis for outpatient treatment monitoring remains questionable; however, if acylcarnitine profiles are measured in the clinical setting, standardized procedures are required for sample collection to be of value.
Collapse
Affiliation(s)
- Gabriela Elizondo
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Dietrich Matern
- Biochemical Genetics Laboratory, Mayo Clinic, Rochester, MN, United States of America
| | - Jerry Vockley
- Department of Pediatrics University of Pittsburgh School of Medicine, Center for Rare Disease Therapy, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States of America
| | - Cary O Harding
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Melanie B Gillingham
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America; Biochemical Genetics Laboratory, Mayo Clinic, Rochester, MN, United States of America.
| |
Collapse
|
37
|
Al-Zohily B, Al-Menhali A, Gariballa S, Haq A, Shah I. Epimers of Vitamin D: A Review. Int J Mol Sci 2020; 21:ijms21020470. [PMID: 31940808 PMCID: PMC7013384 DOI: 10.3390/ijms21020470] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 12/12/2022] Open
Abstract
In this review, we discuss the sources, formation, metabolism, function, biological activity, and potency of C3-epimers (epimers of vitamin D). We also determine the role of epimerase in vitamin D-binding protein (DBP) and vitamin D receptors (VDR) according to different subcellular localizations. The importance of C3 epimerization and the metabolic pathway of vitamin D at the hydroxyl group have recently been recognized. Here, the hydroxyl group at the C3 position is orientated differently from the alpha to beta orientation in space. However, the details of this epimerization pathway are not yet clearly understood. Even the gene encoding for the enzyme involved in epimerization has not yet been identified. Many published research articles have illustrated the biological activity of C3 epimeric metabolites using an in vitro model, but the studies on in vivo models are substantially inadequate. The metabolic stability of 3-epi-1α,25(OH)2D3 has been demonstrated to be higher than its primary metabolites. 3-epi-1 alpha, 25 dihydroxyvitamin D3 (3-epi-1α,25(OH)2D3) is thought to have fewer calcemic effects than non-epimeric forms of vitamin D. Some researchers have observed a larger proportion of total vitamin D as C3-epimers in infants than in adults. Insufficient levels of vitamin D were found in mothers and their newborns when the epimers were not included in the measurement of vitamin D. Oral supplementation of vitamin D has also been found to potentially cause increased production of epimers in mice but not humans. Moreover, routine vitamin D blood tests for healthy adults will not be significantly affected by epimeric interference using LC-MS/MS assays. Recent genetic models also show that the genetic determinants and the potential factors of C3-epimers differ from those of non-C3-epimers.Most commercial immunoassays techniques can lead to inaccurate vitamin D results due to epimeric interference, especially in infants and pregnant women. It is also known that the LC-MS/MS technique can chromatographically separate epimeric and isobaric interference and detect vitamin D metabolites sensitively and accurately. Unfortunately, many labs around the world do not take into account the interference caused by epimers. In this review, various methods and techniques for the analysis of C3-epimers are also discussed. The authors believe that C3-epimers may have an important role to play in clinical research, and further research is warranted.
Collapse
Affiliation(s)
- Bashar Al-Zohily
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain 15551, UAE;
| | - Asma Al-Menhali
- Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, UAE
- Correspondence: (A.A.-M.); (I.S.)
| | - Salah Gariballa
- Internal Medicine, Faculty of Medicine & Health Sciences, United Arab Emirates University, Al Ain 15551, UAE;
| | - Afrozul Haq
- Department of Food Technology, School of Interdisciplinary Sciences and Technology, Jamia Hamdard University, New Delhi-110062, India;
| | - Iltaf Shah
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain 15551, UAE;
- Correspondence: (A.A.-M.); (I.S.)
| |
Collapse
|
38
|
Uda K, Edashige Y, Nishimura R, Shikano Y, Matsui T, Radkov AD, Moe LA. Distribution and evolution of the serine/aspartate racemase family in plants. Phytochemistry 2020; 169:112164. [PMID: 31622858 DOI: 10.1016/j.phytochem.2019.112164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/24/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
Previous studies have shown that several d-amino acids are widely present in plants, and serine racemase (SerR), which synthesizes d-serine in vivo, has already been identified from three plant species. However, the full picture of the d-amino acid synthesis pathway in plants is not well understood. To clarify the distribution of amino acid racemases in plants, we have cloned, expressed and characterized eight SerR homologous genes from five plant species, including green alga. These SerR homologs exhibited racemase activity towards serine or aspartate and were identified on the basis of their maximum activity as SerR or aspartate racemase (AspR). The plant AspR gene is identified for the first time from Medicago truncatula, Manihot esculenta, Solanum lycopersicum, Sphagnum girgensohnii and Spirogyra pratensis. In addition to the AspR gene, three SerR genes are identified in the former three species. Phylogenetic tree analysis showed that SerR and AspR are widely distributed in plants and form a serine/aspartate racemase family cluster. The catalytic efficiency (kcat/Km) of plant AspRs was more than 100 times higher than that of plant SerRs, suggesting that d-aspartate, as well as d-serine, can be synthesized in vivo by AspR. The amino acid sequence alignment and comparison of the chromosomal gene arrangement have revealed that plant AspR genes independently evolved from SerR in each ancestral lineage of plant species by gene duplication and acquisition of two serine residues at position 150 to 152.
Collapse
Affiliation(s)
- Kouji Uda
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan.
| | - Yumika Edashige
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan
| | - Rie Nishimura
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan
| | - Yuuna Shikano
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan
| | - Tohru Matsui
- Laboratory of Plant Taxonomy, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan
| | - Atanas D Radkov
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Luke A Moe
- Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY, 40546-0312, USA
| |
Collapse
|
39
|
Ohshima K, Nojima S, Tahara S, Kurashige M, Kawasaki K, Hori Y, Taniguchi M, Umakoshi Y, Okuzaki D, Wada N, Ikeda JI, Fukusaki E, Morii E. Serine racemase enhances growth of colorectal cancer by producing pyruvate from serine. Nat Metab 2020; 2:81-96. [PMID: 32694681 DOI: 10.1038/s42255-019-0156-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 11/29/2019] [Indexed: 11/09/2022]
Abstract
Serine racemase (SRR) catalyses not only the racemization but also the dehydration of L-serine and D-serine, resulting in the formation of pyruvate and ammonia. Although SRR activity is important in the central nervous system, SRR has not been linked to cancer metabolism before. Here we show that SRR supports proliferation of colorectal-cancer cells. We find that SRR expression is upregulated in colorectal adenoma and adenocarcinoma lesions compared with non-neoplastic mucosa in human colorectal-cancer specimens. SRR-mediated dehydration of serine contributes to the pyruvate pool in colon-cancer cells, enhances proliferation, maintains mitochondrial mass and increases basal reactive oxygen species production, which has anti-apoptotic effects. Moreover, SRR promotes acetylation of histone H3 by maintaining intracellular acetyl-CoA levels. Inhibition of SRR suppresses growth of colorectal tumours in mice and augments the efficacy of 5-fluorouracil treatment. Our findings highlight a previously unknown mechanism through which a racemase supports cancer-cell growth and suggest that SRR might be a molecular target for colorectal-cancer therapy.
Collapse
Affiliation(s)
- Kenji Ohshima
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Shinichiro Tahara
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Masako Kurashige
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Keisuke Kawasaki
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yumiko Hori
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Moyu Taniguchi
- Department of Biotechnology, Osaka University Graduate School of Engineering, Suita, Osaka, Japan
| | - Yutaka Umakoshi
- Department of Biotechnology, Osaka University Graduate School of Engineering, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Naoki Wada
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Diagnostic Pathology, Osaka City University, Osaka, Osaka, Japan
| | - Jun-Ichiro Ikeda
- Department of Diagnostic Pathology, Chiba University Graduate School of Medicine, Chiba, Chiba, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Osaka University Graduate School of Engineering, Suita, Osaka, Japan
| | - Eiichi Morii
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
| |
Collapse
|
40
|
Leung HH, Ng AL, Durand T, Kawasaki R, Oger C, Balas L, Galano JM, Wong IY, Chung-Yung Lee J. Increase in omega-6 and decrease in omega-3 polyunsaturated fatty acid oxidation elevates the risk of exudative AMD development in adults with Chinese diet. Free Radic Biol Med 2019; 145:349-356. [PMID: 31605749 DOI: 10.1016/j.freeradbiomed.2019.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/05/2019] [Accepted: 10/09/2019] [Indexed: 12/19/2022]
Abstract
Appropriate diet is essential for the regulation of age-related macular degeneration (AMD). In particular the type of dietary polyunsaturated fatty acids (PUFA) and poor antioxidant status including carotenoid levels concomitantly contribute to AMD risk. Build-up of oxidative stress in AMD induces PUFA oxidation, and a mix of lipid oxidation products (LOPs) are generated. However, LOPs are not comprehensively evaluated in AMD. LOPs are considered biomarkers of oxidative stress but also contributes to inflammatory response. In this cross-sectional case-control study, plasma omega-6/omega-3 PUFA ratios and antioxidant status (glutathione, superoxide dismutase and catalase), and plasma and urinary LOPs (41 types) were determined to evaluate its odds-ratio in the risk of developing exudative AMD (n = 99) compared to age-gender-matched healthy controls (n = 198) in adults with Chinese diet. The odds ratio of developing exudative AMD increased with LOPs from omega-6 PUFA and decreased from those of omega-3 PUFA. These observations were associated with a high plasma omega-6/omega-3 PUFA ratio and low carotenoid levels. In short, poor PUFA and antioxidant status increased the production of omega-6 PUFA LOPs such as dihomo-isoprostane and dihomo-isofuran, and lowered omega-3 PUFA LOPs such as neuroprostanes due to the high omega-6/omega-3 PUFA ratios; they were also correlated to the risk of AMD development. These findings indicate the generation of specific LOPs is associated with the development of exudative AMD.
Collapse
Affiliation(s)
- Ho Hang Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Alex Lk Ng
- Department of Ophthalmology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Hong Kong Ophthalmic Associates, Hong Kong SAR, China
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, ENSCM, Université de Montpellier, France
| | - Ryo Kawasaki
- Department of Vision Informatics, Osaka University, Japan
| | - Camille Oger
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, ENSCM, Université de Montpellier, France
| | - Laurence Balas
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, ENSCM, Université de Montpellier, France
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, ENSCM, Université de Montpellier, France
| | - Ian Yh Wong
- Department of Ophthalmology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Department of Ophthalmology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - Jetty Chung-Yung Lee
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
41
|
Ran G, Tan D, Zhao J, Fan F, Zhang Q, Wu X, Fan P, Fang X, Lu X. Functionalized polyhydroxyalkanoate nano-beads as a stable biocatalyst for cost-effective production of the rare sugar d-allulose. Bioresour Technol 2019; 289:121673. [PMID: 31260936 DOI: 10.1016/j.biortech.2019.121673] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
d-Allulose is a promising low-calorie sweetener especially for diabetes and obesity patients. The functionalized polyhydroxyalkanoate (PHA) nano-beads decorated with d-tagatose 3-epimerase (DTE) was produced in recombinant endotoxin-free ClearColi, whereby the expression, purification, and immobilization of the active DTE were efficiently combined into one step. The immobilized DTE exhibited remarkable enzyme activity of 649.3 U/g beads and extremely high stability at a harsh working condition (pH 7.0-8.0, 65 °C). When DTE-PHA beads were subjected to enzymatic synthesis of d-allulose, a maximum conversion rate of 33% can be achieved at pH 7.0 and 65 °C for 3 h, and DTE-PHA beads retained about 80% of its initial activity after 8 continuous cycles. Moreover, the d-allulose/d-fructose binary mixture can be simply separated by a single cation exchange resin-equipped chromatography. Taken together, DTE-PHA beads are promising and robust nano-biocatalysts that will remarkably simplify the production procedures of d-allulose, contributing to its cost-effective production.
Collapse
Affiliation(s)
- Ganqiao Ran
- Institute of Bio-Agriculture of Shannxi Province, Xi'an 710043, Shaanxi, People's Republic of China; Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Dan Tan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Jiping Zhao
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Fan Fan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Qiang Zhang
- Institute of Bio-Agriculture of Shannxi Province, Xi'an 710043, Shaanxi, People's Republic of China
| | - Xingjuan Wu
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Peiyao Fan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Xinlei Fang
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Xiaoyun Lu
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China.
| |
Collapse
|
42
|
Petrova YD, Wadda K, Nathubhai A, Yevglevskis M, Mitchell PJ, James TD, Threadgill MD, Woodman TJ, Lloyd MD. Identification of novel small-molecule inhibitors of α-methylacyl-CoA racemase (AMACR; P504S) and structure-activity relationships. Bioorg Chem 2019; 92:103264. [PMID: 31536955 DOI: 10.1016/j.bioorg.2019.103264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S; EC 5.1.99.4) catalyses epimerization of 2-methylacyl-CoAs and is important for the degradation of branched-chain fatty acids and the pharmacological activation of ibuprofen and related drugs. It is also a novel drug target for prostate and other cancers. However, development of AMACR as a drug target has been hampered by the difficulties in assaying enzyme activity. Consequently, reported inhibitors have been rationally designed acyl-CoA esters, which are delivered as their carboxylate prodrugs. The novel colorimetric assay for AMACR based on the elimination of 2,4-dinitrophenolate was developed for high-throughput screening and 20,387 'drug-like compounds' were screened, with a throughput of 768 compounds assayed per day. Pyrazoloquinolines and pyrazolopyrimidines were identified as novel scaffolds and investigated as AMACR inhibitors. The most potent inhibitors have IC50 values of ~2 µM. The pyrazoloquinoline inhibitor 10a displayed uncompetitive inhibition, whilst 10j displayed mixed competitive inhibition. The pyrazolopyrimidine inhibitor 11k displayed uncompetitive inhibition. This is the first report of the identification of specific drug-like small-molecule AMACR inhibitors by high-throughput screening. Pyrazoloquinolines and pyrazolopyrimidines may also be useful as inhibitors of other CoA-utilizing enzymes.
Collapse
Affiliation(s)
- Yoana D Petrova
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Katty Wadda
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; School of Pharmacy and Pharmaceutical Sciences, Sciences Complex, City Campus, Dale Building, Room 121, Sunderland SR1 3SD, UK(1)
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Paul J Mitchell
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| |
Collapse
|
43
|
Cai ZP, Conway LP, Huang YY, Wang WJ, Laborda P, Wang T, Lu AM, Yao HL, Huang K, Flitsch SL, Liu L, Voglmeir J. Enzymatic Synthesis of Trideuterated Sialosides. Molecules 2019; 24:molecules24071368. [PMID: 30965582 PMCID: PMC6479850 DOI: 10.3390/molecules24071368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/21/2022] Open
Abstract
Sialic acids are a family of acidic monosaccharides often found on the termini of cell surface proteins or lipid glycoconjugates of higher animals. Herein we describe the enzymatic synthesis of the two isotopically labeled sialic acid derivatives d3-X-Gal-α-2,3-Neu5Ac and d3-X-Gal-α-2,3-Neu5Gc. Using deuterium oxide as the reaction solvent, deuterium atoms could be successfully introduced during the enzymatic epimerization and aldol addition reactions when the sialosides were generated. NMR and mass spectrometric analyses confirmed that the resulting sialosides were indeed tri-deuterated. These compounds may be of interest as internal standards in liquid chromatography/mass spectrometric assays for biochemical or clinical studies of sialic acids. This was further exemplified by the use of this tri-deuterated sialosides as internal standards for the quantification of sialic acids in meat and egg samples.
Collapse
Affiliation(s)
- Zhi-P Cai
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Louis P Conway
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ying Y Huang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wen J Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Pedro Laborda
- School of Life Sciences, Nantong University, Nantong 226019, China.
| | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ai M Lu
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hong L Yao
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kun Huang
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
| | - Sabine L Flitsch
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
44
|
Roy S, Axelrod HD, Valkenburg KC, Amend S, Pienta KJ. Optimization of prostate cancer cell detection using multiplex tyramide signal amplification. J Cell Biochem 2019; 120:4804-4812. [PMID: 30390333 PMCID: PMC6519224 DOI: 10.1002/jcb.28016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/12/2018] [Indexed: 11/12/2022]
Abstract
Approximately 29 000 men die of prostate cancer (PCa) each year in the United States, and 90% to 100% of them are due to incurable bone metastasis. It is difficult to determine (1) when PCa disseminates in the natural history of the disease; (2) where cancer cell disseminates before becoming overt metastatic lesions; and (3) which tumors are aggressive and which are indolent. Tumor tissue and liquid (blood and bone marrow) biopsies provide important information to answer these questions, but significant limitations exist for immunostaining strategies that assess protein expression in these tissues. Classic immunohistochemistry (IHC) assays can typically assess expression of one or two proteins per tissue section. We have developed a novel immunofluorescence staining protocol to detect a panel of seven proteins on PCa tissue from primary tumor biopsies and metastatic lesion autopsy tissue, as well as cancer cells from liquid biopsies. We used a tyramide-based system to amplify the true signal and optimized the protocol to reduce background signal, thereby boosting the signal-to-noise ratio. Any protein-specific antibody in this protocol can be exchanged for a different validated antibody. This protocol therefore, represents a highly informative and flexible assay that can be used to provide important information about cancer tissue for the purpose of improving detection, diagnosis, and treatment.
Collapse
Affiliation(s)
- Sounak Roy
- The Johns Hopkins University, The Krieger School of Arts & SciencesBaltimoreMaryland
- The James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins University School of MedicineBaltimoreMaryland
| | - Haley D. Axelrod
- The James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins University School of MedicineBaltimoreMaryland
- The Cellular and Molecular Medicine ProgramJohns Hopkins School of MedicineBaltimoreMaryland
| | - Kenneth C. Valkenburg
- The James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins University School of MedicineBaltimoreMaryland
| | - Sarah Amend
- The James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins University School of MedicineBaltimoreMaryland
| | - Kenneth J. Pienta
- The James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins University School of MedicineBaltimoreMaryland
| |
Collapse
|
45
|
Tang CD, Ding PJ, Shi HL, Jia YY, Zhou MZ, Yu HL, Xu JH, Yao LG, Kan YC. One-Pot Synthesis of Phenylglyoxylic Acid from Racemic Mandelic Acids via Cascade Biocatalysis. J Agric Food Chem 2019; 67:2946-2953. [PMID: 30807132 DOI: 10.1021/acs.jafc.8b07295] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phenylglyoxylic acid (PGA) are key building blocks and widely used to synthesize pharmaceutical intermediates or food additives. However, the existing synthetic methods for PGA generally involve toxic cyanide and complex processes. To explore an alternative method for PGA biosynthesis, we envisaged cascade biocatalysis for the one-pot synthesis of PGA from racemic mandelic acid. A novel mandelate racemase named ArMR showing higher expression level (216.9 U·mL-1 fermentation liquor) was cloned from Agrobacterium radiobacter and identified, and six recombinant Escherichia coli strains were engineered to coexpress three enzymes of mandelate racemase, d-mandelate dehydrogenase and l-lactate dehydrogenase, and transform racemic mandelic acid to PGA. Among them, the recombinant E. coli TCD 04, engineered to coexpress three enzymes of ArMR, LhDMDH, and LhLDH, can transform racemic mandelic acid (100 mM) to PGA with 98% conversion. Taken together, we provide a green approach for one-pot biosynthesis of PGA from racemic mandelic acid.
Collapse
Affiliation(s)
- Cun-Duo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Peng-Ju Ding
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| | - Hong-Ling Shi
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| | - Yuan-Yuan Jia
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| | - Mao-Zhi Zhou
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Lun-Guang Yao
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| | - Yun-Chao Kan
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| |
Collapse
|
46
|
Juneja A, Zhang G, Jin YS, Singh V. Bioprocessing and technoeconomic feasibility analysis of simultaneous production of d-psicose and ethanol using engineered yeast strain KAM-2GD. Bioresour Technol 2019; 275:27-34. [PMID: 30576911 DOI: 10.1016/j.biortech.2018.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/07/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
The objective of this study was to analyze the processing and technoeconomic feasibility of coproduction of d-psicose and ethanol in a modified dry grind ethanol process. The yeast strain was constructed by expressing d-psicose 3-epimerases (DPE) in Sachharomyces cerevisiae. The strain was capable of converting d-fructose to d-psicose at 55 °C with a conversion efficiency of 26.6%. A comprehensive process model for modified dry grind ethanol plant with 396,000 MT/yr corn processing capacity was developed using SuperPro Designer. Predicted ethanol and d-psicose yields were 390.4 L and 75.3 kg per MT of corn, with total annual production of 154.6 million L and 29,835 MT respectively. The capital investment for the plant was estimated as 150.3 million USD with total operating cost of 85.2 million USD/yr. The unit production cost and minimum selling price of d-psicose with an internal rate of return of 15% were calculated as $0.43/kg and $1.29/kg respectively.
Collapse
Affiliation(s)
- Ankita Juneja
- Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Guochang Zhang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Vijay Singh
- Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
| |
Collapse
|
47
|
Abstract
The donor substrates for the biosynthesis of bacterial polysaccharides include UDP-Glc/Gal and UDP-GlcNAc/GalNAc. The conversion of these nucleotide sugars is catalyzed by 4-epimerases. The wbpP gene of Pseudomonas aeruginosa encodes a 4-epimerase that has a preference for UDP-GlcNAc/GalNAc as substrates. Other 4-epimerases have broad specificities or preference for UDP-Glc/Gal. We have developed coupled assays where the 4-epimerase product is used as a donor substrate for glycosyltransferases that are highly specific for the nucleotide sugar structure. We describe here a method for the study of substrate specificity of WbpP, using coupled assays employing four different glycosyltransferases. These protocols can be applied to the identification and characterization of novel 4-epimerases and to determine their substrate specificities.
Collapse
Affiliation(s)
- Sulav Sharma
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Carole Creuzenet
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Kenneth F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Inka Brockhausen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
| |
Collapse
|
48
|
Etheridge T, Straus J, Ritter MA, Jarrard DF, Huang W. Semen AMACR protein as a novel method for detecting prostate cancer. Urol Oncol 2018; 36:532.e1-532.e7. [PMID: 30337219 DOI: 10.1016/j.urolonc.2018.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 09/02/2018] [Accepted: 09/12/2018] [Indexed: 11/18/2022]
Abstract
BACKGROUND Alpha methylacyl A coenzyme racemase (AMACR) has shown to be an excellent immunohistological biomarker for prostate cancer (CaP). Given the connection between prostate and urethra, we hypothesized that semen ejaculate would be an ideal specimen for detection of CaP specific biomarkers, such as AMACR. This study explores the detection of semen AMACR protein in men with and without CaP. METHODS Semen ejaculates from 28 biopsy proven CaP patients prior to radical prostatectomy and 15 age-comparable controls were analyzed. An indirect sandwich ELISA chemiluminescence assay was used to detect semen AMACR, PSA, and Matriptase proteins. Tissue AMACR protein was quantified in 12 corresponding prostatectomy specimens using automated quantitative analysis (AQUA). RESULTS Semen AMACR protein was detected in 23 of 28 (82%) CaP patients and 23 of 24 (96%) CaP patients with significant tumor volume (>0.5 cc or 0.3 g). Among the 5 cancer patients with undetectable semen AMACR, 4 patients had small tumor volumes (<1% or 0.3 g). Semen AMACR protein was also detected in 7 of 15 (47%) control noncancer patients. Using 76 ng/ml as a cutoff value, 20 of 28 (71%) patients and 20 of 24 (83%) patients with significant tumor volume were positive for semen AMACR protein, whereas only 5 of 15 (33%) age-comparable controls were positive. AMACR levels degrade with time. CONCLUSIONS This is the first study to demonstrate that AMACR protein is detectable in semen ejaculate. The higher AMACR levels detected in cancer patients suggests that semen AMACR protein may be useful as a noninvasive test for prostate cancer. Further validation is warranted.
Collapse
Affiliation(s)
- Tyler Etheridge
- Department of Urology, University of Wisconsin-Madison, Madison, WI
| | - Jane Straus
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI
| | - Mark A Ritter
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI
| | - David F Jarrard
- Department of Urology, University of Wisconsin-Madison, Madison, WI; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI.
| |
Collapse
|
49
|
Sharma S, Ding Y, Jarrell KF, Brockhausen I. Identification and characterization of the 4-epimerase AglW from the archaeon Methanococcus maripaludis. Glycoconj J 2018; 35:525-535. [PMID: 30293150 DOI: 10.1007/s10719-018-9845-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/11/2018] [Accepted: 09/24/2018] [Indexed: 11/27/2022]
Abstract
Archaea are ubiquitous single-cell microorganisms that have often adapted to harsh conditions and play important roles in biogeochemical cycles with potential applications in biotechnology. Methanococcus maripaludis, a methane-producing archaeon, is motile through multiple archaella on its cell surface. The major structural proteins (archaellins) of the archaellum are glycoproteins, modified with N-linked tetrasaccharides that are essential for the proper assembly and function of archaella. The aglW gene, encoding the putative 4-epimerase AglW, plays a key role in the synthesis of the tetrasaccharide. The goal of our work was to biochemically demonstrate the 4-epimerase activity of AglW, and to develop assays to determine its substrate specificity and properties. We carried out assays using UDP-Galactose, UDP-Glucose, UDP-N-acetylglucosamine, UDP-N-acetylgalactosamine and N-acetylglucosamine/N-acetylgalactosamine-diphosphate - lipid as substrates, coupled with specific glycosyltransferases. We showed that AglW has a broad specificity towards UDP-sugars and that Tyr151 within a conserved YxxxK sequon is essential for the 4-epimerase function of AglW. The glycosyltransferase-coupled assays are generally useful for the identification and specificity studies of novel 4-epimerases.
Collapse
Affiliation(s)
- Sulav Sharma
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L 3N6, Canada
| | - Yan Ding
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L 3N6, Canada
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L 3N6, Canada
| | - Inka Brockhausen
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L 3N6, Canada.
| |
Collapse
|
50
|
Liu B, Fang S, Ma X, Bai Z, Hu K. Backbone and side-chain chemical shift assignments of MarH, a critical intermediary epimerase for biosynthesis of Maremycins in Streptomyces. Biomol NMR Assign 2018; 12:335-338. [PMID: 30054867 DOI: 10.1007/s12104-018-9835-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/25/2018] [Indexed: 06/08/2023]
Abstract
MarH is an essential epimerase that catalyzes the isomerization of 3R-β-methyl-indolepyruvate (β-MeInPy) to 3S-β-MeInPy, which is the important precursor for biosynthesis of Maremycins. Biophysical study of the structure of MarH would be informative for better understanding of its catalytic mechanism and feasible application of the enzyme in isomerization reaction. Here, we report the backbone and side-chain NMR chemical shift assignments of MarH, which lays a foundation for further structural and mechanical study of the enzyme.
Collapse
Affiliation(s)
- Bin Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiqi Fang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofang Ma
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiqiang Bai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kaifeng Hu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, 650201, Yunnan, China.
| |
Collapse
|