2
|
Xia J, Xin W, Wang F, Xie W, Liu Y, Xu J. Cloning and Characterization of Fructose-1,6-Bisphosphate Aldolase from Euphausia superba. Int J Mol Sci 2022; 23:ijms231810478. [PMID: 36142390 PMCID: PMC9499490 DOI: 10.3390/ijms231810478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) is a highly conserved enzyme that is involved in glycolysis and gluconeogenesis. In this study, we cloned the fructose-1,6-bisphosphate aldolase gene from Euphausia superba (EsFBA). The full-length cDNA sequence of EsFBA is 1098 bp long and encodes a 365-amino-acid protein. The fructose-1,6-bisphosphate aldolase gene was expressed in Escherichia coli (E. coli). A highly purified protein was obtained using HisTrap HP affinity chromatography and size-exclusion chromatography. The predicted three-dimensional structure of EsFBA showed a 65.66% homology with human aldolase, whereas it had the highest homology (84.38%) with the FBA of Penaeus vannamei. Recombinant EsFBA had the highest activity at 45 °C and pH 7.0 in phosphate buffer. By examining the activity of metal ions and EDTA, we found that the effect of metal ions and EDTA on EsFBA's enzyme activity was not significant, while the presence of borohydride severely reduced the enzymatic activity; thus, EsFBA was confirmed to be a class I aldolase. Furthermore, targeted mutations at positions 34, 147, 188, and 230 confirmed that they are key amino acid residues for EsFBA.
Collapse
Affiliation(s)
- Jikun Xia
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Wanmeng Xin
- State Key Laboratory of Biocatalysts and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Fang Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Wancui Xie
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yi Liu
- State Key Laboratory of Biocatalysts and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
- Correspondence: (Y.L.); (J.X.)
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
- Correspondence: (Y.L.); (J.X.)
| |
Collapse
|
3
|
Dushanan R, Weerasinghe S, Dissanayake DP, Senthilnithy R. An In-Silico Approach to Evaluate the Inhibitory Potency of Selected Hydroxamic Acid Derivatives on Zinc-Dependent Histone Deacetylase Enzyme. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Histone deacetylase (HDAC) enzymes modify the histone by removing the acetyl group from the lysine residues, known as histone deacetylation. HDACs have been involved in altering gene expressions, resulting in cancer cells in the body. This study focuses on HDAC inhibitors’ impact on histone deacetylase-like protein (HDLP) stability through computational techniques. Molecular dynamics (MD) analyses were used to examine the atomic-level description of drug binding sites and how the HDAC inhibitors change the HDLP enzyme environment. In this study, two hydroxamic acid-derived inhibitors, such as [Formula: see text]-Carboxycinnamic acid bis-hydroxamide (CBHA) and scriptaid (GCK1026), were selected to examine the inhibition ability in terms with suberanilohydroxamic acid (SAHA) as a reference drug. The crystal structure of the HDLP was downloaded from the Protein Data Bank. The structures of inhibitors were optimized using the G09W package. Docking studies were done by AutoDock-Vina, and the resultant complex was used to initiate MD studies. The trajectories obtained from MD simulation were used to perform the structural analysis. Root-mean-square deviation (RMSD), radius of gyration, hydrogen bond, binding free energy and interaction energy studies revealed that the stability of HDLP-SAHA and HDLP-CBHA is higher than the free HDLP enzyme. The HDLP-CBHA complex shows an increased number of hydrogen bonds (5), high MM-PBSA binding free energy ([Formula: see text][Formula: see text]kJ/mol), high interaction energy ([Formula: see text][Formula: see text]kJ/mol), and an increased number of alpha-helical amino acids (130) compared with HDLP-SAHA. It concluded that the CBHA has the relatively same potential as SAHA to inhibit the HDLP. Consequently, the use of CBHA in clinical application is recommended through this in-silico method.
Collapse
Affiliation(s)
- R. Dushanan
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda 10250, Sri Lanka
| | - S. Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00700, Sri Lanka
| | - D. P. Dissanayake
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00700, Sri Lanka
| | - R. Senthilnithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda 10250, Sri Lanka
| |
Collapse
|
4
|
Pirovich DB, Da’dara AA, Skelly PJ. Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target. Front Mol Biosci 2021; 8:719678. [PMID: 34458323 PMCID: PMC8385298 DOI: 10.3389/fmolb.2021.719678] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/31/2021] [Indexed: 01/01/2023] Open
Abstract
Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
Collapse
Affiliation(s)
- David B. Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
| | | | | |
Collapse
|
7
|
Feng S, Jiao K, Guo H, Jiang M, Hao J, Wang H, Shen C. Succinyl-proteome profiling of Dendrobium officinale, an important traditional Chinese orchid herb, revealed involvement of succinylation in the glycolysis pathway. BMC Genomics 2017; 18:598. [PMID: 28797234 PMCID: PMC5553593 DOI: 10.1186/s12864-017-3978-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 08/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lysine succinylation is a ubiquitous and important protein post-translational modification in various eukaryotic and prokaryotic cells. However, its functions in Dendrobium officinale, an important traditional Chinese orchid herb with high polysaccharide contents, are largely unknown. RESULTS In our study, LC-MS/MS was used to identify the peptides that were enriched by immune-purification with a high-efficiency succinyl-lysine antibody. In total, 314 lysine succinylation sites in 207 proteins were identified. A gene ontology analysis showed that these proteins are associated with a wide range of cellular functions, from metabolic processes to stimuli responses. Moreover, two types of conserved succinylation motifs, '***Ksuc******K**' and '****EKsuc***', were identified. Our data showed that lysine succinylation occurred on five key enzymes in the glycolysis pathway. The numbers of average succinylation sites on these five enzymes in plants were lower than those in bacteria and mammals. Interestingly, two active site amino acids residues, K103 and K225, could be succinylated in fructose-bisphosphate aldolase, indicating a potential function of lysine succinylation in the regulation of glycolytic enzyme activities. Furthermore, the protein-protein interaction network for the succinylated proteins showed that several functional terms, such as glycolysis, TCA cycle, oxidative phosphorylation and ribosome, are consisted. CONCLUSIONS Our results provide the first comprehensive view of the succinylome of D. officinale and may accelerate future biological investigations of succinylation in the synthesis of polysaccharides, which are major active ingredients.
Collapse
Affiliation(s)
- Shangguo Feng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Kaili Jiao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Hong Guo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Mengyi Jiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Juan Hao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| |
Collapse
|
9
|
Noon JB, Hewezi T, Maier TR, Simmons C, Wei JZ, Wu G, Llaca V, Deschamps S, Davis EL, Mitchum MG, Hussey RS, Baum TJ. Eighteen New Candidate Effectors of the Phytonematode Heterodera glycines Produced Specifically in the Secretory Esophageal Gland Cells During Parasitism. PHYTOPATHOLOGY 2015; 105:1362-72. [PMID: 25871857 DOI: 10.1094/phyto-02-15-0049-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, is the number one pathogen of soybean (Glycine max). This nematode infects soybean roots and forms an elaborate feeding site in the vascular cylinder. H. glycines produces an arsenal of effector proteins in the secretory esophageal gland cells. More than 60 H. glycines candidate effectors were identified in previous gland-cell-mining projects. However, it is likely that additional candidate effectors remained unidentified. With the goal of identifying remaining H. glycines candidate effectors, we constructed and sequenced a large gland cell cDNA library resulting in 11,814 expressed sequence tags. After bioinformatic filtering for candidate effectors using a number of criteria, in situ hybridizations were performed in H. glycines whole-mount specimens to identify candidate effectors whose mRNA exclusively accumulated in the esophageal gland cells, which is a hallmark of many nematode effectors. This approach resulted in the identification of 18 new H. glycines esophageal gland-cell-specific candidate effectors. Of these candidate effectors, 11 sequences were pioneers without similarities to known proteins while 7 sequences had similarities to functionally annotated proteins in databases. These putative homologies provided the bases for the development of hypotheses about potential functions in the parasitism process.
Collapse
Affiliation(s)
- Jason B Noon
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Tarek Hewezi
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Thomas R Maier
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Carl Simmons
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Jun-Zhi Wei
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Gusui Wu
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Victor Llaca
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Stéphane Deschamps
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Eric L Davis
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Melissa G Mitchum
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Richard S Hussey
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Thomas J Baum
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| |
Collapse
|