1
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Taylor J, Ayres-Galhardo PH, Brown BL. Elucidating the Role of Human ALAS2 C-terminal Mutations Resulting in Loss of Function and Disease. Biochemistry 2024; 63:1636-1646. [PMID: 38888931 PMCID: PMC11223264 DOI: 10.1021/acs.biochem.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
The conserved enzyme aminolevulinic acid synthase (ALAS) initiates heme biosynthesis in certain bacteria and eukaryotes by catalyzing the condensation of glycine and succinyl-CoA to yield aminolevulinic acid. In humans, the ALAS isoform responsible for heme production during red blood cell development is the erythroid-specific ALAS2 isoform. Owing to its essential role in erythropoiesis, changes in human ALAS2 (hALAS2) function can lead to two different blood disorders. X-linked sideroblastic anemia results from loss of ALAS2 function, while X-linked protoporphyria results from gain of ALAS2 function. Interestingly, mutations in the ALAS2 C-terminal extension can be implicated in both diseases. Here, we investigate the molecular basis for enzyme dysfunction mediated by two previously reported C-terminal loss-of-function variants, hALAS2 V562A and M567I. We show that the mutations do not result in gross structural perturbations, but the enzyme stability for V562A is decreased. Additionally, we show that enzyme stability moderately increases with the addition of the pyridoxal 5'-phosphate (PLP) cofactor for both variants. The variants display differential binding to PLP and the individual substrates compared to wild-type hALAS2. Although hALAS2 V562A is a more active enzyme in vitro, it is less efficient concerning succinyl-CoA binding. In contrast, the M567I mutation significantly alters the cooperativity of substrate binding. In combination with previously reported cell-based studies, our work reveals the molecular basis by which hALAS2 C-terminal mutations negatively affect ALA production necessary for proper heme biosynthesis.
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Affiliation(s)
- Jessica
L. Taylor
- Department
of Biochemistry, Center for Structural Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Pedro H. Ayres-Galhardo
- Department
of Biochemistry, Center for Structural Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Breann L. Brown
- Department
of Biochemistry, Center for Structural Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
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2
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Zhang DK, Song KY, Yan YQ, Zheng JT, Xu J, Da LT, Xu MJ. Structural and mechanistic investigations on CC bond forming α-oxoamine synthase allowing L-glutamate as substrate. Int J Biol Macromol 2024; 268:131696. [PMID: 38642679 DOI: 10.1016/j.ijbiomac.2024.131696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/23/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Carbon‑carbon (C-C) bonds serve as the fundamental structural backbone of organic molecules. As a critical CC bond forming enzyme, α-oxoamine synthase is responsible for the synthesis of α-amino ketones by performing the condensation reaction between amino acids and acyl-CoAs. We previously identified an α-oxoamine synthase (AOS), named as Alb29, involved in albogrisin biosynthesis in Streptomyces albogriseolus MGR072. This enzyme belongs to the α-oxoamine synthase family, a subfamily under the pyridoxal 5'-phosphate (PLP) dependent enzyme superfamily. In this study, we report the crystal structures of Alb29 bound to PLP and L-Glu, which provide the atomic-level structural insights into the substrate recognition by Alb29. We discover that Alb29 can catalyze the amino transformation from L-Gln to L-Glu, besides the condensation of L-Glu with β-methylcrotonyl coenzyme A. Subsequent structural analysis has revealed that one flexible loop in Alb29 plays an important role in both amino transformation and condensation. Based on the crystal structure of the S87G mutant in the loop region, we capture two distinct conformations of the flexible loop in the active site, compared with the wild-type Alb29. Our study offers valuable insights into the catalytic mechanism underlying substrate recognition of Alb29.
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Affiliation(s)
- Dai-Ke Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Kai-Yuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ya-Qian Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jian-Ting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
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3
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Zdubek A, Maliszewska I. On the Possibility of Using 5-Aminolevulinic Acid in the Light-Induced Destruction of Microorganisms. Int J Mol Sci 2024; 25:3590. [PMID: 38612403 PMCID: PMC11011456 DOI: 10.3390/ijms25073590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Antimicrobial photodynamic inactivation (aPDI) is a method that specifically kills target cells by combining a photosensitizer and irradiation with light at the appropriate wavelength. The natural amino acid, 5-aminolevulinic acid (5-ALA), is the precursor of endogenous porphyrins in the heme biosynthesis pathway. This review summarizes the recent progress in understanding the biosynthetic pathways and regulatory mechanisms of 5-ALA synthesis in biological hosts. The effectiveness of 5-ALA-aPDI in destroying various groups of pathogens (viruses, fungi, yeasts, parasites) was presented, but greater attention was focused on the antibacterial activity of this technique. Finally, the clinical applications of 5-ALA in therapies using 5-ALA and visible light (treatment of ulcers and disinfection of dental canals) were described.
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Affiliation(s)
| | - Irena Maliszewska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370 Wrocław, Poland;
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4
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Ashley B, Baslé A, Sajjad M, el Ashram A, Kelis P, Marles-Wright J, Campopiano DJ. Versatile Chemo-Biocatalytic Cascade Driven by a Thermophilic and Irreversible C-C Bond-Forming α-Oxoamine Synthase. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:7997-8002. [PMID: 37266354 PMCID: PMC10230504 DOI: 10.1021/acssuschemeng.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/24/2023] [Indexed: 06/03/2023]
Abstract
We report a chemo-biocatalytic cascade for the synthesis of substituted pyrroles, driven by the action of an irreversible, thermostable, pyridoxal 5'-phosphate (PLP)-dependent, C-C bond-forming biocatalyst (ThAOS). The ThAOS catalyzes the Claisen-like condensation between various amino acids and acyl-CoA substrates to generate a range of α-aminoketones. These products are reacted with β-keto esters in an irreversible Knorr pyrrole reaction. The determination of the 1.6 Å resolution crystal structure of the PLP-bound form of ThAOS lays the foundation for future engineering and directed evolution. This report establishes the AOS family as useful and versatile C-C bond-forming biocatalysts.
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Affiliation(s)
- Ben Ashley
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Arnaud Baslé
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne NE2 4HH, United Kingdom
| | - Mariyah Sajjad
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Ahmed el Ashram
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Panayiota Kelis
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Jon Marles-Wright
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne NE2 4HH, United Kingdom
| | - Dominic J. Campopiano
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
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5
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Tran JU, Brown BL. The yeast ALA synthase C-terminus positively controls enzyme structure and function. Protein Sci 2023; 32:e4600. [PMID: 36807942 PMCID: PMC10031213 DOI: 10.1002/pro.4600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023]
Abstract
5-Aminolevulinic acid synthase (ALAS) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the first and rate-limiting step of heme biosynthesis in α-proteobacteria and several non-plant eukaryotes. All ALAS homologs contain a highly conserved catalytic core, but eukaryotes also have a unique C-terminal extension that plays a role in enzyme regulation. Several mutations in this region are implicated in multiple blood disorders in humans. In Saccharomyces cerevisiae ALAS (Hem1), the C-terminal extension wraps around the homodimer core to contact conserved ALAS motifs proximal to the opposite active site. To determine the importance of these Hem1 C-terminal interactions, we determined the crystal structure of S. cerevisiae Hem1 lacking the terminal 14 amino acids (Hem1 ΔCT). With truncation of the C-terminal extension, we show structurally and biochemically that multiple catalytic motifs become flexible, including an antiparallel β-sheet important to Fold-Type I PLP-dependent enzymes. The changes in protein conformation result in an altered cofactor microenvironment, decreased enzyme activity and catalytic efficiency, and ablation of subunit cooperativity. These findings suggest that the eukaryotic ALAS C-terminus has a homolog-specific role in mediating heme biosynthesis, indicating a mechanism for autoregulation that can be exploited to allosterically modulate heme biosynthesis in different organisms.
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Affiliation(s)
- Jenny U. Tran
- Department of BiochemistryVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Breann L. Brown
- Department of BiochemistryVanderbilt University School of MedicineNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt University School of MedicineNashvilleTennesseeUSA
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6
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Ma Z, Li D, Yang X, Liang J, Zhu Y. Case report: An infant boy with X-linked sideroblastic anaemia successfully treated by umbilical cord blood haematopoietic stem cell transplantation. Front Genet 2022; 13:1009988. [DOI: 10.3389/fgene.2022.1009988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/28/2022] [Indexed: 11/16/2022] Open
Abstract
X-linked sideroblastic anaemia (XLSA) is an inherited disorder caused by mutations in genes encoding proteins involved in the biosynthesis of haem. The pathogenic gene, as well as the pathogenesis and diagnosis of XLSA, have been fully elucidated in previous studies. However, only a few new advances have been made in managing XLSA in recent years, and blood transfusion remains the primary treatment. We report a case of umbilical cord blood haematopoietic stem cell transplantation in a male infant diagnosed with XLSA who was born with asphyxia due to severe anaemia. Early hepatic vein occlusion occurred after transplantation. However, this complication was rapidly controlled after active treatment, and the child’s quality of life improved significantly. Haematopoietic stem cell transplantation is a promising alternative treatment for XLSA.
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7
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Abstract
Heme (protoheme IX) is an essential cofactor for a large variety of proteins whose functions vary from one electron reactions to binding gases. While not ubiquitous, heme is found in the great majority of known life forms. Unlike most cofactors that are acquired from dietary sources, the vast majority of organisms that utilize heme possess a complete pathway to synthesize the compound. Indeed, dietary heme is most frequently utilized as an iron source and not as a source of heme. In Nature there are now known to exist three pathways to synthesize heme. These are the siroheme dependent (SHD) pathway which is the most ancient, but least common of the three; the coproporphyrin dependent (CPD) pathway which with one known exception is found only in gram positive bacteria; and the protoporphyrin dependent (PPD) pathway which is found in gram negative bacteria and all eukaryotes. All three pathways share a core set of enzymes to convert the first committed intermediate, 5-aminolevulinate (ALA) into uroporphyrinogen III. In the current review all three pathways are reviewed as well as the two known pathways to synthesize ALA. In addition, interesting features of some heme biosynthesis enzymes are discussed as are the regulation and disorders of heme biosynthesis.
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Affiliation(s)
- Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Department of Microbiology, University of Georgia, Athens, GA 30602-1111, USA
| | - Amy E Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, USA
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8
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Müller M, Germer P, Andexer JN. Biocatalytic One-Carbon Transfer – A Review. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1719884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractThis review provides an overview of different C1 building blocks as substrates of enzymes, or part of their cofactors, and the resulting functionalized products. There is an emphasis on the broad range of possibilities of biocatalytic one-carbon extensions with C1 sources of different oxidation states. The identification of uncommon biosynthetic strategies, many of which might serve as templates for synthetic or biotechnological applications, towards one-carbon extensions is supported by recent genomic and metabolomic progress and hence we refer principally to literature spanning from 2014 to 2020.1 Introduction2 Methane, Methanol, and Methylamine3 Glycine4 Nitromethane5 SAM and SAM Ylide6 Other C1 Building Blocks7 Formaldehyde and Glyoxylate as Formaldehyde Equivalents8 Cyanide9 Formic Acid10 Formyl-CoA and Oxalyl-CoA11 Carbon Monoxide12 Carbon Dioxide13 Conclusions
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9
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Kawaguchi J, Mori H, Iwai N, Wachi M. A secondary metabolic enzyme functioned as an evolutionary seed of a primary metabolic enzyme. Mol Biol Evol 2022; 39:6651898. [PMID: 35904937 PMCID: PMC9356726 DOI: 10.1093/molbev/msac164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The antibiotic alaremycin has a structure that resembles that of 5-aminolevulinic acid (ALA), a universal precursor of porphyrins, and inhibits porphyrin biosynthesis. Genome sequencing of the alaremycin-producing bacterial strain and enzymatic analysis revealed that the first step of alaremcyin biosynthesis is catalysed by the enzyme, AlmA, which exhibits a high degree of similarity to 5-aminolevulinate synthase (ALAS) expressed by animals, protozoa, fungi and α-proteobacteria. Site-directed mutagenesis of AlmA revealed that the substitution of two amino acids residues around the substrate binding pocket transformed its substrate specificity from that of alaremycin precursor synthesis to ALA synthesis. To estimate the evolutionary trajectory of AlmA and ALAS, we performed an ancestral sequence reconstitution analysis based on a phylogenetic tree of AlmA and ALAS. The reconstructed common ancestral enzyme of AlmA and ALAS exhibited alaremycin precursor synthetic activity, rather than ALA synthetic activity. These results suggest that ALAS evolved from an AlmA-like enzyme. We propose a new evolutionary hypothesis in which a non-essential secondary metabolic enzyme acts as an 'evolutionary seed' to generate an essential primary metabolic enzyme.
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Affiliation(s)
- Jun Kawaguchi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hikaru Mori
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Noritaka Iwai
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Masaaki Wachi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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10
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Yien YY, Perfetto M. Regulation of Heme Synthesis by Mitochondrial Homeostasis Proteins. Front Cell Dev Biol 2022; 10:895521. [PMID: 35832791 PMCID: PMC9272004 DOI: 10.3389/fcell.2022.895521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Heme plays a central role in diverse, life-essential processes that range from ubiquitous, housekeeping pathways such as respiration, to highly cell-specific ones such as oxygen transport by hemoglobin. The regulation of heme synthesis and its utilization is highly regulated and cell-specific. In this review, we have attempted to describe how the heme synthesis machinery is regulated by mitochondrial homeostasis as a means of coupling heme synthesis to its utilization and to the metabolic requirements of the cell. We have focused on discussing the regulation of mitochondrial heme synthesis enzymes by housekeeping proteins, transport of heme intermediates, and regulation of heme synthesis by macromolecular complex formation and mitochondrial metabolism. Recently discovered mechanisms are discussed in the context of the model organisms in which they were identified, while more established work is discussed in light of technological advancements.
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11
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Radka CD, Miller DJ, Frank MW, Rock CO. Biochemical characterization of the first step in sulfonolipid biosynthesis in Alistipes finegoldii. J Biol Chem 2022; 298:102195. [PMID: 35760102 PMCID: PMC9304779 DOI: 10.1016/j.jbc.2022.102195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/01/2022] Open
Abstract
Sulfonolipids are unusual lipids found in the outer membranes of Gram-negative bacteria in the phylum Bacteroidetes. Sulfonolipid and its deacylated derivative, capnine, are sulfur analogs of ceramide-1-phosphate and sphingosine-1-phosphate, respectively; thus, sulfonolipid biosynthesis is postulated to be similar to the sphingolipid biosynthetic pathway. Here, we identify the first enzyme in sulfonolipid synthesis in Alistipes finegoldii, an anaerobic gut commensal bacterium, as the product of the alfi_1224 gene, cysteate acyl-acyl carrier protein (ACP) transferase (SulA). We show SulA catalyzes the condensation of acyl-ACP and cysteate (3-sulfo-alanine) to form 3-ketocapnine. Acyl-CoA is a poor substrate. We show SulA has a bound pyridoxal phosphate (PLP) cofactor that undergoes a spectral redshift in the presence of cysteate, consistent with the transition of the lysine-aldimine complex to a substrate-aldimine complex. Furthermore, the SulA crystal structure shows the same prototypical fold found in bacterial serine palmitoyltransferases (Spt), enveloping the PLP cofactor bound to Lys251. We observed the SulA and Spt active sites are identical except for Lys281 in SulA, which is an alanine in Spt. Additionally, SulA(K281A) is catalytically inactive, but binds cysteate and forms the external aldimine normally, highlighting the structural role of the Lys281 side chain in walling off the active site from bulk solvent. Finally, the electropositive groove on the protein surface adjacent to the active site entrance provides a landing pad for the electronegative acyl-ACP surface. Taken together, these data identify the substrates, products, and mechanism of SulA, the PLP-dependent condensing enzyme that catalyzes the first step in sulfonolipid synthesis in a gut commensal bacterium.
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Affiliation(s)
- Christopher D Radka
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA.
| | - Darcie J Miller
- Departments of, Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
| | - Matthew W Frank
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
| | - Charles O Rock
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
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12
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Zhang T, Chen J, Zheng P, Gong W, Sun J, Liu H. Crystal structure of 5-Aminolevulinate synthase HemA from Rhodopseudomonas palustris presents multiple conformations. Biochem Biophys Res Commun 2022; 609:100-104. [DOI: 10.1016/j.bbrc.2022.04.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 11/02/2022]
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13
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Congenital sideroblastic anemia model due to ALAS2 mutation is susceptible to ferroptosis. Sci Rep 2022; 12:9024. [PMID: 35637209 PMCID: PMC9151922 DOI: 10.1038/s41598-022-12940-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
X-linked sideroblastic anemia (XLSA), the most common form of congenital sideroblastic anemia, is caused by a germline mutation in the erythroid-specific 5-aminolevulinate synthase (ALAS2) gene. In XLSA, defective heme biosynthesis leads to ring sideroblast formation because of excess mitochondrial iron accumulation. In this study, we introduced ALAS2 missense mutations on human umbilical cord blood-derived erythroblasts; hereafter, we refer to them as XLSA clones. XLSA clones that differentiated into mature erythroblasts showed an increased frequency of ring sideroblast formation with impaired hemoglobin biosynthesis. The expression profiling revealed significant enrichment of genes involved in ferroptosis, which is a form of regulated cell death induced by iron accumulation and lipid peroxidation. Notably, treatment with erastin, a ferroptosis inducer, caused a higher proportion of cell death in XLSA clones. XLSA clones exhibited significantly higher levels of intracellular lipid peroxides and enhanced expression of BACH1, a regulator of iron metabolism and potential accelerator of ferroptosis. In XLSA clones, BACH1 repressed genes involved in iron metabolism and glutathione synthesis. Collectively, defective heme biosynthesis in XLSA clones could confer enhanced BACH1 expression, leading to increased susceptibility to ferroptosis. The results of our study provide important information for the development of novel therapeutic targets for XLSA.
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14
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Tran JU, Brown BL. Structural Basis for Allostery in PLP-dependent Enzymes. Front Mol Biosci 2022; 9:884281. [PMID: 35547395 PMCID: PMC9081730 DOI: 10.3389/fmolb.2022.884281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are found ubiquitously in nature and are involved in a variety of biological pathways, from natural product synthesis to amino acid and glucose metabolism. The first structure of a PLP-dependent enzyme was reported over 40 years ago, and since that time, there is a steady wealth of structural and functional information revealed for a wide array of these enzymes. A functional mechanism that is gaining more appreciation due to its relevance in drug design is that of protein allostery, where binding of a protein or ligand at a distal site influences the structure, organization, and function at the active site. Here, we present a review of current structure-based mechanisms of allostery for select members of each PLP-dependent enzyme family. Knowledge of these mechanisms may have a larger potential for identifying key similarities and differences among enzyme families that can eventually be exploited for therapeutic development.
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Affiliation(s)
- Jenny U. Tran
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Breann L. Brown
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
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15
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Bissell AU, Rautschek J, Hoefgen S, Raguž L, Mattern DJ, Saeed N, Janevska S, Jojić K, Huang Y, Kufs JE, Herboeck B, Guo H, Hillmann F, Beemelmanns C, Valiante V. Biosynthesis of the Sphingolipid Inhibitors Sphingofungins in Filamentous Fungi Requires Aminomalonate as a Metabolic Precursor. ACS Chem Biol 2022; 17:386-394. [PMID: 35023724 DOI: 10.1021/acschembio.1c00839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sphingofungins belong to a group of structurally related sphingolipid inhibitors produced by fungi, which specifically inhibit serine palmitoyl transferases, enzymes catalyzing the initial step during sphingolipid biosynthesis. Sphingolipids are integral parts of the eukaryotic cell membrane, and disturbances in their homeostasis have been linked to various human diseases. It has been suggested that external interventions, via sphingolipid inhibitors, may represent a promising approach for alternative therapies. Here, we identified and elucidated the biosynthetic gene cluster responsible for the biosynthesis of sphingofungins B, C, and D in Aspergillus fumigatus. Moreover, in vitro analyses have shown that sphingofungin biosynthesis starts with the condensation of a C18 polyketide with the uncommon substrate aminomalonate. Furthermore, the investigations on sphingofungin E and F produced by Paecilomyces variotii pointed out that different aminomalonate derivatives are used as substrates for those chemical variants. This research boosts knowledge on the general biosynthesis of sphingolipid inhibitors in fungi.
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Affiliation(s)
- Alexander U. Bissell
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Julia Rautschek
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Sandra Hoefgen
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Luka Raguž
- Chemical Biology of Microbe−Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Derek J. Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Nauman Saeed
- Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Slavica Janevska
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Katarina Jojić
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Ying Huang
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Johann E. Kufs
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Bio Pilot Plant, Hans Knöll Institute (HKI), Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Barbara Herboeck
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Huijuan Guo
- Chemical Biology of Microbe−Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Falk Hillmann
- Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe−Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Vito Valiante
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
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Taylor JL, Brown BL. Structural basis for dysregulation of aminolevulinic acid synthase in human disease. J Biol Chem 2022; 298:101643. [PMID: 35093382 PMCID: PMC8892079 DOI: 10.1016/j.jbc.2022.101643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/19/2023] Open
Abstract
Heme is a critical biomolecule that is synthesized in vivo by several organisms such as plants, animals, and bacteria. Reflecting the importance of this molecule, defects in heme biosynthesis underlie several blood disorders in humans. Aminolevulinic acid synthase (ALAS) initiates heme biosynthesis in α-proteobacteria and nonplant eukaryotes. Debilitating and painful diseases such as X-linked sideroblastic anemia and X-linked protoporphyria can result from one of more than 91 genetic mutations in the human erythroid-specific enzyme ALAS2. This review will focus on recent structure-based insights into human ALAS2 function in health and how it dysfunctions in disease. We will also discuss how certain genetic mutations potentially result in disease-causing structural perturbations. Furthermore, we use thermodynamic and structural information to hypothesize how the mutations affect the human ALAS2 structure and categorize some of the unique human ALAS2 mutations that do not respond to typical treatments, that have paradoxical in vitro activity, or that are highly intolerable to changes. Finally, we will examine where future structure-based insights into the family of ALA synthases are needed to develop additional enzyme therapeutics.
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Affiliation(s)
- Jessica L Taylor
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Breann L Brown
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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17
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Belton S, Lamari N, Jermiin LS, Mariscal V, Flores E, McCabe PF, Ng CKY. Genetic and lipidomic analyses suggest that Nostoc punctiforme, a plant-symbiotic cyanobacterium, does not produce sphingolipids. Access Microbiol 2022; 4:000306. [PMID: 35252750 PMCID: PMC8895605 DOI: 10.1099/acmi.0.000306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/23/2021] [Indexed: 11/21/2022] Open
Abstract
Sphingolipids, a class of amino-alcohol-based lipids, are well characterized in eukaryotes and in some anaerobic bacteria. However, the only sphingolipids so far identified in cyanobacteria are two ceramides (i.e., an acetylsphingomyelin and a cerebroside), both based on unbranched, long-chain base (LCB) sphingolipids in Scytonema julianum and Moorea producens, respectively. The first step in de novo sphingolipid biosynthesis is the condensation of l-serine with palmitoyl-CoA to produce 3-keto-diyhydrosphingosine (KDS). This reaction is catalyzed by serine palmitoyltransferase (SPT), which belongs to a small family of pyridoxal phosphate-dependent α-oxoamine synthase (AOS) enzymes. Based on sequence similarity to molecularly characterized bacterial SPT peptides, we identified a putative SPT (Npun_R3567) from the model nitrogen-fixing, plant-symbiotic cyanobacterium, Nostoc punctiforme strain PCC 73102 (ATCC 29133). Gene expression analysis revealed that Npun_R3567 is induced during late-stage diazotrophic growth in N. punctiforme. However, Npun_R3567 could not produce the SPT reaction product, 3-keto-diyhydrosphingosine (KDS), when heterologously expressed in Escherichia coli. This agreed with a sphingolipidomic analysis of N. punctiforme cells, which revealed that no LCBs or ceramides were present. To gain a better understanding of Npun_R3567, we inferred the phylogenetic position of Npun_R3567 relative to other bacterial AOS peptides. Rather than clustering with other bacterial SPTs, Npun_R3567 and the other cyanobacterial BioF homologues formed a separate, monophyletic group. Given that N. punctiforme does not appear to possess any other gene encoding an AOS enzyme, it is altogether unlikely that N. punctiforme is capable of synthesizing sphingolipids. In the context of cross-kingdom symbiosis signalling in which sphingolipids are emerging as important regulators, it appears unlikely that sphingolipids from N. punctiforme play a regulatory role during its symbiotic association with plants.
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Affiliation(s)
- Samuel Belton
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
- Present address: DBN Plant Molecular Biology Lab, National Botanic Gardens of Ireland, Dublin, Ireland
| | - Nadia Lamari
- Present address: Philip Morris International, Quai Jeanrenaud 3, 2000, Neuchâtel, Switzerland
- UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
| | - Lars S. Jermiin
- Research School of Biology, Australian National University, Canberra, ACT 2600, Australia
- UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
| | - Vicente Mariscal
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Avda. Américo Vespucio 49, 41092 Seville, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Avda. Américo Vespucio 49, 41092 Seville, Spain
| | - Paul F. McCabe
- UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD Centre for Plant Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
| | - Carl K. Y. Ng
- UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD Centre for Plant Science, University College Dublin, Belfield, Dublin D4, Ireland
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18
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Ziemann M, Lim SC, Kang Y, Samuel S, Sanchez IL, Gantier M, Stojanovski D, McKenzie M. MicroRNA-101-3p Modulates Mitochondrial Metabolism via the Regulation of Complex II Assembly. J Mol Biol 2021; 434:167361. [PMID: 34808225 DOI: 10.1016/j.jmb.2021.167361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/17/2021] [Accepted: 11/11/2021] [Indexed: 12/27/2022]
Abstract
MicroRNA-101-3p (miR-101-3p) is a tumour suppressor that regulates cancer proliferation and apoptotic signalling. Loss of miR-101-3p increases the expression of the Polycomb Repressive Complex 2 (PRC2) subunit enhancer of zeste homolog 2 (EZH2), resulting in alterations to the epigenome and enhanced tumorigenesis. MiR-101-3p has also been shown to modulate various aspects of cellular metabolism, however little is known about the mechanisms involved. To investigate the metabolic pathways that are regulated by miR-101-3p, we performed transcriptome and functional analyses of osteosarcoma cells transfected with miR-101-3p. We found that miR-101-3p downregulates multiple mitochondrial processes, including oxidative phosphorylation, pyruvate metabolism, the citric acid cycle and phospholipid metabolism. We also found that miR-101-3p transfection disrupts the transcription of mitochondrial DNA (mtDNA) via the downregulation of the mitochondrial transcription initiation complex proteins TFB2M and Mic60. These alterations in transcript expression disrupt mitochondrial function, with significant decreases in both basal (54%) and maximal (67%) mitochondrial respiration rates. Native gel electrophoresis revealed that this diminished respiratory capacity was associated with reduced steady-state levels of mature succinate dehydrogenase (complex II), with a corresponding reduction of complex II enzymatic activity. Furthermore, miR-101-3p transfection reduced the expression of the SDHB subunit, with a concomitant disruption of the assembly of the SDHC subunit into mature complex II. Overall, we describe a new role for miR-101-3p as a modulator of mitochondrial metabolism via its regulation of multiple mitochondrial processes, including mtDNA transcription and complex II biogenesis.
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Affiliation(s)
- Mark Ziemann
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 3216 Geelong, Australia. https://twitter.com/@mdziemann
| | - Sze Chern Lim
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168 Melbourne, Australia
| | - Yilin Kang
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 3052 Melbourne, Australia
| | - Sona Samuel
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria 3002, Australia
| | - Isabel Lopez Sanchez
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria 3002, Australia; Ophthalmology, University of Melbourne, Department of Surgery Melbourne, Victoria 3000, Australia. https://twitter.com/@DrIsabelLopez
| | - Michael Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168 Melbourne, Australia; Department of Molecular and Translational Science, Monash University, 3168 Melbourne, Australia. https://twitter.com/@GantierLab
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 3052 Melbourne, Australia
| | - Matthew McKenzie
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 3216 Geelong, Australia; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168 Melbourne, Australia; Department of Molecular and Translational Science, Monash University, 3168 Melbourne, Australia.
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19
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Chang HY, Lo LH, Lan YH, Hong MX, Chan YT, Ko TP, Huang YR, Cheng TH, Liaw CC. Structural insights into the substrate selectivity of α-oxoamine synthases from marine Vibrio sp. QWI-06. Colloids Surf B Biointerfaces 2021; 210:112224. [PMID: 34838420 DOI: 10.1016/j.colsurfb.2021.112224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/09/2021] [Accepted: 11/13/2021] [Indexed: 12/12/2022]
Abstract
Pyridoxal phosphate (PLP)-dependent α-oxoamine synthases are generally believed to be responsible for offloading and elongating polyketides or catalyzing the condensation of amino acids and acyl-CoA thioester substrates, such as serine into sphingolipids and cysteate into sulfonolipids. Previously, we discovered vitroprocines, which are tyrosine- and phenylalanine-polyketide derivatives, as potential new antibiotics from the genus Vibrio. Using bioinformatics analysis, we identified putative genes of PLP-dependent enzyme from marine Vibrio sp. QWI-06, implying a capability to produce amino-polyketide derivatives. One of these genes was cloned, and the recombinant protein, termed Vibrio sp. QWI-06 α-oxoamine synthases-1 (VsAOS1), was overexpressed for structural and biochemical characterization. The crystal structure of the dimeric VsAOS1 was determined at 1.8-Å resolution in the presence of L-glycine. The electron density map indicated a glycine molecule occupying the pyridoxal binding site in one monomer, suggesting a snapshot of the initiation process upon the loading of amino acid substrate. In mass spectrometry analysis, VsAOS1 strictly acted to condense L-glycine with C12 or C16 acyl-CoA, including unsaturated acyl analog. Furthermore, a single residue replacement of VsAOS1 (G243S) allowed the enzyme to generate sphingoid derivative when L-serine and lauroyl-CoA were used as substrates. Our data elucidate the mechanism of substrate binding and selectivity by the VsAOS1 and provide a thorough understanding of the molecular basis for the amino acid preference of AOS members.
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Affiliation(s)
- Hsin-Yang Chang
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Li-Hua Lo
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Hsuan Lan
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Mao-Xuan Hong
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yuen Ting Chan
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Ru Huang
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tien-Hsing Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan; Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan.
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20
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Azacitidine is a potential therapeutic drug for pyridoxine-refractory female X-linked sideroblastic anemia. Blood Adv 2021; 6:1100-1114. [PMID: 34781359 PMCID: PMC8864662 DOI: 10.1182/bloodadvances.2021005664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/04/2021] [Indexed: 01/19/2023] Open
Abstract
A patient-derived iPSC model recapitulates defective erythroid maturation in female XLSA. Azacitidine reactivates the silent wild-type ALAS2 allele and ameliorates inefficient erythropoiesis in iPSC-derived HPCs from female XLSA.
X-linked sideroblastic anemia (XLSA) is associated with mutations in the erythroid-specific δ-aminolevulinic acid synthase (ALAS2) gene. Treatment of XLSA is mainly supportive, except in patients who are pyridoxine responsive. Female XLSA often represents a late onset of severe anemia, mostly related to the acquired skewing of X chromosome inactivation. In this study, we successfully generated active wild-type and mutant ALAS2-induced pluripotent stem cell (iPSC) lines from the peripheral blood cells of an affected mother and 2 daughters in a family with pyridoxine-resistant XLSA related to a heterozygous ALAS2 missense mutation (R227C). The erythroid differentiation potential was severely impaired in active mutant iPSC lines compared with that in active wild-type iPSC lines. Most of the active mutant iPSC-derived erythroblasts revealed an immature morphological phenotype, and some showed dysplasia and perinuclear iron deposits. In addition, globin and HO-1 expression and heme biosynthesis in active mutant erythroblasts were severely impaired compared with that in active wild-type erythroblasts. Furthermore, genes associated with erythroblast maturation and karyopyknosis showed significantly reduced expression in active mutant erythroblasts, recapitulating the maturation defects. Notably, the erythroid differentiation ability and hemoglobin expression of active mutant iPSC-derived hematopoietic progenitor cells (HPCs) were improved by the administration of δ-aminolevulinic acid, verifying the suitability of the cells for drug testing. Administration of a DNA demethylating agent, azacitidine, reactivated the silent, wild-type ALAS2 allele in active mutant HPCs and ameliorated the erythroid differentiation defects, suggesting that azacitidine is a potential novel therapeutic drug for female XLSA. Our patient-specific iPSC platform provides novel biological and therapeutic insights for XLSA.
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21
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Nomura K, Kitagawa Y, Aihara M, Ohki Y, Furuyama K, Hirokawa T. Heme-dependent recognition of 5-aminolevulinate synthase by the human mitochondrial molecular chaperone ClpX. FEBS Lett 2021; 595:3019-3029. [PMID: 34704252 DOI: 10.1002/1873-3468.14214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/21/2021] [Accepted: 10/15/2021] [Indexed: 11/08/2022]
Abstract
The caseinolytic mitochondrial matrix peptidase chaperone subunit (ClpX) plays an important role in the heme-dependent regulation of 5-aminolevulinate synthase (ALAS1), a key enzyme in heme biosynthesis. However, the mechanisms underlying the role of ClpX in this process remain unclear. In this in vitro study, we confirmed the direct binding between ALAS1 and ClpX in a heme-dependent manner. The substitution of C108 P109 [CP motif 3 (CP3)] with A108 A109 in ALAS1 resulted in a loss of ability to bind ClpX. Computational disorder analyses revealed that CP3 was located in a potential intrinsically disordered protein region (IDPR). Thus, we propose that conditional disorder-to-order transitions in the IDPRs of ALAS1 may represent key mechanisms underlying the heme-dependent recognition of ALAS1 by ClpX.
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Affiliation(s)
- Kazumi Nomura
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Yu Kitagawa
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Marina Aihara
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Yusuke Ohki
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | | | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Japan.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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22
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[New mutation of congenital sideroblastic anemia: a case report and literature review]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:603-605. [PMID: 34455750 PMCID: PMC8408491 DOI: 10.3760/cma.j.issn.0253-2727.2021.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Kwarteng A, Asiedu E, Sylverken A, Larbi A, Mubarik Y, Apprey C. In silico drug repurposing for filarial infection predicts nilotinib and paritaprevir as potential inhibitors of the Wolbachia 5'-aminolevulinic acid synthase. Sci Rep 2021; 11:8455. [PMID: 33875732 PMCID: PMC8055890 DOI: 10.1038/s41598-021-87976-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
Filarial infections affect millions of individuals and are responsible for some notorious disabilities. Current treatment options involve repeated mass drug administrations, which have been met with several challenges despite some successes. Administration of doxycycline, an anti-Wolbachia agent, has shown clinical effectiveness but has several limitations, including long treatment durations and contraindications. We describe the use of an in silico drug repurposing approach to screening a library of over 3200 FDA-approved medications against the filarial endosymbiont, Wolbachia. We target the enzyme which catalyzes the first step of heme biosynthesis in the Wolbachia. This presents an opportunity to inhibit heme synthesis, which leads to depriving the filarial worm of heme, resulting in a subsequent macrofilaricidal effect. High throughput virtual screening, molecular docking and molecular simulations with binding energy calculations led to the identification of paritaprevir and nilotinib as potential anti-Wolbachia agents. Having higher binding affinities to the catalytic pocket than the natural substrate, these drugs have the structural potential to bind and engage active site residues of the wolbachia 5'-Aminolevulinic Acid Synthase. We hereby propose paritaprevir and nilotinib for experimental validations as anti-Wolbachia agents.
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Affiliation(s)
- Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana. .,Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana.
| | - Ebenezer Asiedu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
| | - Augustina Sylverken
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
| | - Amma Larbi
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
| | - Yusif Mubarik
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
| | - Charles Apprey
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
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24
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Huang J, Ge M, Shao Y, Wang M, Jin P, Huo J, Li X, Zhang J, Nie N, Zheng Y. A hemizygous p.R204Q mutation in the ALAS2 gene underlies X-linked sideroblastic anemia in an adult Chinese Han man. BMC Med Genomics 2021; 14:107. [PMID: 33858445 PMCID: PMC8048311 DOI: 10.1186/s12920-021-00950-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/23/2021] [Indexed: 12/04/2022] Open
Abstract
Background X-linked sideroblastic anemia (XLSA) is the most common form of congenital sideroblastic anemia (CSA), and is associated with the mutations in the 5-aminolevulinate synthase 2 (ALAS2). The genetic basis of more than 40% of CSA cases remains unknown. Methods A two-generation Chinese family with XLSA was studied by next-generation sequencing to identify the underlying CSA-related mutations. Results In the study, we identified a missense ALAS2 R204Q mutation in a hemizygous Chinese Han man and in his heterozygous daughter. The male proband presented clinical manifestations at 38 years old and had a good response to pyridoxine. Conclusions XLSA, as a hereditary disease, can present clinical manifestations later in lives, for adult male patients with ringed sideroblasts and hypochromic anemia, it should be evaluated with gene analyses to exclude CSA. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00950-x.
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Affiliation(s)
- Jinbo Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
| | - Meili Ge
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China.
| | - Yingqi Shao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
| | - Min Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
| | - Peng Jin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
| | - Jiali Huo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
| | - Xingxin Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
| | - Jing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
| | - Neng Nie
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
| | - Yizhou Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, People's Republic of China
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25
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Gayathri SC, Manoj N. Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases. J Mol Biol 2020; 432:166692. [PMID: 33122004 DOI: 10.1016/j.jmb.2020.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023]
Abstract
PLP-dependent enzymes catalyze a plethora of chemical reactions affecting diverse physiological functions. Here we report the structural determinants of the reaction mechanism in a Group II PLP-dependent decarboxylase by assigning two early intermediates. The in-crystallo complexes of the PLP bound form, and the Dunathan and quinonoid intermediates, allowed direct observation of the active site interactions. The structures reveal that a subtle rearrangement of a conserved Arg residue in concert with a water-mediated interaction with the carboxylate of the Dunathan intermediate, appears to directly stabilize the alignment and facilitate the release of CO2 to yield the quinonoid. Modeling indicates that the conformational change of a dynamic catalytic loop to a closed form controls a conserved network of hydrogen bond interactions between catalytic residues to protonate the quinonoid. Our results provide a structural framework to elucidate mechanistic roles of residues that govern reaction specificity and catalysis in PLP-dependent decarboxylation.
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Affiliation(s)
- Subash Chellam Gayathri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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Uminski K, Houston DS, Hartley JN, Liu J, Cuvelier GDE, Israels SJ. Clinical characterization and hematopoietic stem cell transplant outcomes for congenital sideroblastic anemia caused by a novel pathogenic variant in SLC25A38. Pediatr Blood Cancer 2020; 67:e28623. [PMID: 32790119 DOI: 10.1002/pbc.28623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Congenital sideroblastic anemia (CSA) constitutes an uncommon category of inherited anemia often associated with pathologic iron accumulation. Pathogenic variants in several genes have been identified as causative for CSA. Autosomal recessive pathogenic variants in the mitochondrial glycine transporter SLC25A38 have been implicated in a subset of patients with CSA. PROCEDURE We describe seven individuals of Canadian Cree descent with a known or inferred homozygous novel founder missense variant in SLC25A38 (c.560G>A, p.Arg187Gln). RESULTS All individuals presented as young children (median age 6 months) with severe microcytic, hypochromic anemia associated with pretransfusion iron overload, requiring red cell transfusion support and iron chelation. Six individuals received pyridoxine supplementation; two demonstrating transient partial responses. Three individuals underwent allogeneic hematopoietic stem cell transplantation (HSCT). One individual with significant iron loading died in the posttransplant period due to complications of sepsis. The other two individuals remain transfusion-free following HSCT. CONCLUSIONS Despite a common genetic etiology, phenotypic variability was noted in this cohort. A transient response to pyridoxine was noted in two individuals but should not be considered a long-term therapeutic strategy. HSCT was curative when performed before significant iron loading occurred. Early identification of CSA and timely HSCT can result in excellent long-term outcomes.
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Affiliation(s)
- Kelsey Uminski
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Donald S Houston
- Department of Internal Medicine, Section of Hematology and Medical Oncology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jessica N Hartley
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jing Liu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Geoffrey D E Cuvelier
- Departments of Pediatric Hematology-Oncology, Cancer Care Manitoba, and Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sara J Israels
- Departments of Pediatric Hematology-Oncology, Cancer Care Manitoba, and Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
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Harding CR, Sidik SM, Petrova B, Gnädig NF, Okombo J, Herneisen AL, Ward KE, Markus BM, Boydston EA, Fidock DA, Lourido S. Genetic screens reveal a central role for heme metabolism in artemisinin susceptibility. Nat Commun 2020; 11:4813. [PMID: 32968076 PMCID: PMC7511413 DOI: 10.1038/s41467-020-18624-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/03/2020] [Indexed: 01/26/2023] Open
Abstract
Artemisinins have revolutionized the treatment of Plasmodium falciparum malaria; however, resistance threatens to undermine global control efforts. To broadly explore artemisinin susceptibility in apicomplexan parasites, we employ genome-scale CRISPR screens recently developed for Toxoplasma gondii to discover sensitizing and desensitizing mutations. Using a sublethal concentration of dihydroartemisinin (DHA), we uncover the putative transporter Tmem14c whose disruption increases DHA susceptibility. Screens performed under high doses of DHA provide evidence that mitochondrial metabolism can modulate resistance. We show that disrupting a top candidate from the screens, the mitochondrial protease DegP2, lowers porphyrin levels and decreases DHA susceptibility, without significantly altering parasite fitness in culture. Deleting the homologous gene in P. falciparum, PfDegP, similarly lowers heme levels and DHA susceptibility. These results expose the vulnerability of heme metabolism to genetic perturbations that can lead to increased survival in the presence of DHA.
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Affiliation(s)
- Clare R Harding
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Saima M Sidik
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Boryana Petrova
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Nina F Gnädig
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Kurt E Ward
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Benedikt M Markus
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Kim HS, Lohmar JM, Busman M, Brown DW, Naumann TA, Divon HH, Lysøe E, Uhlig S, Proctor RH. Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium. BMC Genomics 2020; 21:510. [PMID: 32703172 PMCID: PMC7376913 DOI: 10.1186/s12864-020-06896-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Sphingolipids are structural components and signaling molecules in eukaryotic membranes, and many organisms produce compounds that inhibit sphingolipid metabolism. Some of the inhibitors are structurally similar to the sphingolipid biosynthetic intermediate sphinganine and are referred to as sphinganine-analog metabolites (SAMs). The mycotoxins fumonisins, which are frequent contaminants in maize, are one family of SAMs. Due to food and feed safety concerns, fumonisin biosynthesis has been investigated extensively, including characterization of the fumonisin biosynthetic gene cluster in the agriculturally important fungi Aspergillus and Fusarium. Production of several other SAMs has also been reported in fungi, but there is almost no information on their biosynthesis. There is also little information on how widely SAM production occurs in fungi or on the extent of structural variation of fungal SAMs. RESULTS Using fumonisin biosynthesis as a model, we predicted that SAM biosynthetic gene clusters in fungi should include a polyketide synthase (PKS), an aminotransferase and a dehydrogenase gene. Surveys of genome sequences identified five putative clusters with this three-gene combination in 92 of 186 Fusarium species examined. Collectively, the putative SAM clusters were distributed widely but discontinuously among the species. We propose that the SAM5 cluster confers production of a previously reported Fusarium SAM, 2-amino-14,16-dimethyloctadecan-3-ol (AOD), based on the occurrence of AOD production only in species with the cluster and on deletion analysis of the SAM5 cluster PKS gene. We also identified SAM clusters in 24 species of other fungal genera, and propose that one of the clusters confers production of sphingofungin, a previously reported Aspergillus SAM. CONCLUSION Our results provide a genomics approach to identify novel SAM biosynthetic gene clusters in fungi, which should in turn contribute to identification of novel SAMs with applications in medicine and other fields. Information about novel SAMs could also provide insights into the role of SAMs in the ecology of fungi. Such insights have potential to contribute to strategies to reduce fumonisin contamination in crops and to control crop diseases caused by SAM-producing fungi.
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Affiliation(s)
- Hye-Seon Kim
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Jessica M Lohmar
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Mark Busman
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Daren W Brown
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Todd A Naumann
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | | | - Erik Lysøe
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | | | - Robert H Proctor
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA.
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Chun SW, Narayan ARH. Biocatalytic, Stereoselective Deuteration of α-Amino Acids and Methyl Esters. ACS Catal 2020; 10:7413-7418. [PMID: 34430066 DOI: 10.1021/acscatal.0c01885] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
α-2H amino acids are valuable precursors toward labeled pharmaceutical agents and tools for studying biological systems; however, these molecules are costly to purchase and challenging to synthesize in a site- and stereoselective manner. Here, we show that an α-oxo-amine synthase that evolved for saxitoxin biosynthesis, SxtA AONS, is capable of producing a range of α-2H amino acids and esters site- and stereoselectively using D2O as the deuterium source. Additionally, we demonstrate the utility of this operationally simple reaction on preparative scale in the stereoselective chemoenzymatic synthesis of a deuterated analog of safinamide, a drug used to treat Parkinson's disease.
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Ravindra N, Athiyarath R, S E, S S, Kulkarni U, N A F, Korula A, Shaji RV, George B, Edison ES. Novel frameshift variant (c.409dupG) in SLC25A38 is a common cause of congenital sideroblastic anaemia in the Indian subcontinent. J Clin Pathol 2020; 74:157-162. [PMID: 32605921 DOI: 10.1136/jclinpath-2020-206647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 01/19/2023]
Abstract
AIMS Congenital sideroblastic anaemias (CSAs) are a group of rare disorders with the presence of ring sideroblasts in the bone marrow. Pathogenic variants are inherited in an autosomal recessive/X-linked fashion. The study was aimed at characterising the spectrum of mutations in SLC25A38 and ALAS2 genes in sideroblastic anaemia patients, exploring the genotype-phenotype correlation and identifying the haplotype associated with any recurrent mutation. PATIENTS AND METHODS Twenty probable CSA patients were retrospectively analysed for genetic variants in ALAS2 and SLC25A38 genes by direct bidirectional sequencing. Real-time PCR was used to quantify gene expression in a case with promoter region variant in ALAS2. Three single nucleotide polymorphisms were used to establish the haplotype associated with a recurrent variant in the SLC25A38 gene. RESULTS Six patients had causative variants in ALAS2 (30%) and 11 had variants in SLC25A38 (55%). The ALAS2 mutated cases presented at a significantly later age than the SLC25A38 cases. A frameshift variant in SLC25A38 (c.409dupG) was identified in six unrelated patients and was a common variant in our population exhibiting 'founder effect'. CONCLUSION This is the largest series of sideroblastic anaemia cases with molecular characterisation from the Indian subcontinent.
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Affiliation(s)
- Niveditha Ravindra
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rekha Athiyarath
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Eswari S
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Sumithra S
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Uday Kulkarni
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Fouzia N A
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anu Korula
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ramachandran V Shaji
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
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Bailey HJ, Bezerra GA, Marcero JR, Padhi S, Foster WR, Rembeza E, Roy A, Bishop DF, Desnick RJ, Bulusu G, Dailey HA, Yue WW. Human aminolevulinate synthase structure reveals a eukaryotic-specific autoinhibitory loop regulating substrate binding and product release. Nat Commun 2020; 11:2813. [PMID: 32499479 PMCID: PMC7272653 DOI: 10.1038/s41467-020-16586-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
5'-aminolevulinate synthase (ALAS) catalyzes the first step in heme biosynthesis, generating 5'-aminolevulinate from glycine and succinyl-CoA. Inherited frameshift indel mutations of human erythroid-specific isozyme ALAS2, within a C-terminal (Ct) extension of its catalytic core that is only present in higher eukaryotes, lead to gain-of-function X-linked protoporphyria (XLP). Here, we report the human ALAS2 crystal structure, revealing that its Ct-extension folds onto the catalytic core, sits atop the active site, and precludes binding of substrate succinyl-CoA. The Ct-extension is therefore an autoinhibitory element that must re-orient during catalysis, as supported by molecular dynamics simulations. Our data explain how Ct deletions in XLP alleviate autoinhibition and increase enzyme activity. Crystallography-based fragment screening reveals a binding hotspot around the Ct-extension, where fragments interfere with the Ct conformational dynamics and inhibit ALAS2 activity. These fragments represent a starting point to develop ALAS2 inhibitors as substrate reduction therapy for porphyria disorders that accumulate toxic heme intermediates.
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Affiliation(s)
- Henry J Bailey
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Gustavo A Bezerra
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Jason R Marcero
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Siladitya Padhi
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Ltd, Hyderabad, 500081, India
| | - William R Foster
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Elzbieta Rembeza
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Arijit Roy
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Ltd, Hyderabad, 500081, India
| | - David F Bishop
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert J Desnick
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Ltd, Hyderabad, 500081, India
| | - Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
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Abstract
Modified tetrapyrroles are large macrocyclic compounds, consisting of diverse conjugation and metal chelation systems and imparting an array of colors to the biological structures that contain them. Tetrapyrroles represent some of the most complex small molecules synthesized by cells and are involved in many essential processes that are fundamental to life on Earth, including photosynthesis, respiration, and catalysis. These molecules are all derived from a common template through a series of enzyme-mediated transformations that alter the oxidation state of the macrocycle and also modify its size, its side-chain composition, and the nature of the centrally chelated metal ion. The different modified tetrapyrroles include chlorophylls, hemes, siroheme, corrins (including vitamin B12), coenzyme F430, heme d1, and bilins. After nearly a century of study, almost all of the more than 90 different enzymes that synthesize this family of compounds are now known, and expression of reconstructed operons in heterologous hosts has confirmed that most pathways are complete. Aside from the highly diverse nature of the chemical reactions catalyzed, an interesting aspect of comparative biochemistry is to see how different enzymes and even entire pathways have evolved to perform alternative chemical reactions to produce the same end products in the presence and absence of oxygen. Although there is still much to learn, our current understanding of tetrapyrrole biogenesis represents a remarkable biochemical milestone that is summarized in this review.
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Affiliation(s)
- Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
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Li J, Chen L, Lin Y, Ru K. Novel mutations in the ALAS2 gene from patients with X-linked sideroblastic anemia. Int J Lab Hematol 2020; 42:e160-e163. [PMID: 32297424 DOI: 10.1111/ijlh.13214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/09/2020] [Accepted: 03/29/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Jing Li
- SINO-US Diagnostics, Tianjin, China
| | | | - Yani Lin
- SINO-US Diagnostics, Tianjin, China
| | - Kun Ru
- SINO-US Diagnostics, Tianjin, China
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From Synthesis to Utilization: The Ins and Outs of Mitochondrial Heme. Cells 2020; 9:cells9030579. [PMID: 32121449 PMCID: PMC7140478 DOI: 10.3390/cells9030579] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 12/14/2022] Open
Abstract
Heme is a ubiquitous and essential iron containing metallo-organic cofactor required for virtually all aerobic life. Heme synthesis is initiated and completed in mitochondria, followed by certain covalent modifications and/or its delivery to apo-hemoproteins residing throughout the cell. While the biochemical aspects of heme biosynthetic reactions are well understood, the trafficking of newly synthesized heme—a highly reactive and inherently toxic compound—and its subsequent delivery to target proteins remain far from clear. In this review, we summarize current knowledge about heme biosynthesis and trafficking within and outside of the mitochondria.
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Stojanovski BM, Hunter GA, Na I, Uversky VN, Jiang RHY, Ferreira GC. 5-Aminolevulinate synthase catalysis: The catcher in heme biosynthesis. Mol Genet Metab 2019; 128:178-189. [PMID: 31345668 PMCID: PMC6908770 DOI: 10.1016/j.ymgme.2019.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/27/2019] [Accepted: 06/07/2019] [Indexed: 01/26/2023]
Abstract
5-Aminolevulinate (ALA) synthase (ALAS), a homodimeric pyridoxal-5'-phosphate (PLP)-dependent enzyme, catalyzes the first step of heme biosynthesis in metazoa, fungi and α-proteobacteria. In this review, we focus on the advances made in unraveling the mechanism of the ALAS-catalyzed reaction during the past decade. The interplay between the PLP cofactor and the protein moiety determines and modulates the multi-intermediate reaction cycle of ALAS, which involves the decarboxylative condensation of two substrates, glycine and succinyl-CoA. Substrate binding and catalysis are rapid, and product (ALA) release dominates the overall ALAS kinetic mechanism. Interconversion between a catalytically incompetent, open conformation and a catalytically competent, closed conformation is linked to ALAS catalysis. Reversion to the open conformation, coincident with ALA dissociation, defines the slowest step of the reaction cycle. These findings were further substantiated by introducing seven mutations in the16-amino acid loop that gates the active site, yielding an ALAS variant with a greatly increased rate of catalytic turnover and heightened specificity constants for both substrates. Recently, molecular dynamics (MD) simulation analysis of various dimeric ALAS forms revealed that the seven active site loop mutations caused the proteins to adopt different conformations. In particular, the emergence of a β-strand in the mutated loop, which interacted with two preexisting β-strands to form an anti-parallel three-stranded β-sheet, conferred the murine heptavariant with a more stable open conformation and prompted faster product release than wild-type mALAS2. Moreover, the dynamics of the mALAS2 active site loop anti-correlated with that of the 35 amino acid C-terminal sequence. This led us to propose that this C-terminal extension, which is absent in prokaryotic ALASs, finely tunes mammalian ALAS activity. Based on the above results, we extend our previous proposal to include that discovery of a ligand inducing the mammalian C-terminal extension to fold offers a good prospect for the development of a new drug for X-linked protoporphyria and/or other porphyrias associated with enhanced ALAS activity and/or porphyrin accumulation.
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Affiliation(s)
- Bosko M Stojanovski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Gregory A Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Insung Na
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
| | - Rays H Y Jiang
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Gloria C Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA; Department of Chemistry, College of Arts and Sciences, University of South Florida, Tampa, FL 33612, USA.
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Rebets Y, Nadmid S, Paulus C, Dahlem C, Herrmann J, Hübner H, Rückert C, Kiemer AK, Gmeiner P, Kalinowski J, Müller R, Luzhetskyy A. Perquinoline A–C: neuartige bakterielle Tetrahydroisochinoline mit einer bemerkenswerten Biosynthese. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuriy Rebets
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Suvd Nadmid
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Constanze Paulus
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Charlotte Dahlem
- Department of Pharmacy Pharmaceutical Biology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Jennifer Herrmann
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
| | - Harald Hübner
- Department of Chemistry and Pharmacy Friedrich-Alexander-Universität Erlangen-Nürnberg Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Christian Rückert
- Center for Biotechnology – CeBiTec University of Bielefeld Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Alexandra K. Kiemer
- Department of Pharmacy Pharmaceutical Biology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy Friedrich-Alexander-Universität Erlangen-Nürnberg Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Jörn Kalinowski
- Center for Biotechnology – CeBiTec University of Bielefeld Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Rolf Müller
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
| | - Andriy Luzhetskyy
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
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Mouterde LM, Stewart JD. Application of Acetyl-CoA synthetase from Methanothermobacter thermautotrophicus to non-native substrates. Enzyme Microb Technol 2019; 128:67-71. [DOI: 10.1016/j.enzmictec.2019.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
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Jeong SY, Jin H, Chang JH. Crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe. PLoS One 2019; 14:e0221975. [PMID: 31465495 PMCID: PMC6715241 DOI: 10.1371/journal.pone.0221975] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/18/2019] [Indexed: 01/01/2023] Open
Abstract
L-aspartate aminotransferase is a pyridoxal 5'-phosphate-dependent transaminase that catalyzes reversible transfer of an α-amino group from aspartate to α-ketoglutarate or from glutamate to oxaloacetate. L-aspartate aminotransferase not only mediates amino acid and carbohydrate metabolism but also regulates the cellular level of amino acids by catalyzing amino acid degradation and biosynthesis. To expand our structural information, we determined the crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe at 2.1 Å resolution. A structural comparison between two yeast L-aspartate aminotransferases revealed conserved enzymatic mechanism mediated by the open-closed conformational change. Compared with higher eukaryotic species, L-aspartate aminotransferases showed distinguishable inter-subunit interaction between the N-terminal arm and a large domain of the opposite subunit. Interestingly, structural homology search showed varied conformation of the N-terminal arm among 71 structures of the family. Therefore, we classified pyridoxal 5'-phosphate-dependent enzymes into eight subclasses based on the structural feature of N-terminal arms. In addition, structure and sequence comparisons showed strong relationships among the eight subclasses. Our results may provide insights into structure-based evolutionary aspects of pyridoxal 5'-phosphate-dependent enzymes.
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Affiliation(s)
- Soo Yeon Jeong
- Department of Biology Education, Kyungpook National University, Daegu, Republic of Korea
| | - Hyeonseok Jin
- Research Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (HJ); (JHC)
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu, Republic of Korea
- Research Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (HJ); (JHC)
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Rebets Y, Nadmid S, Paulus C, Dahlem C, Herrmann J, Hübner H, Rückert C, Kiemer AK, Gmeiner P, Kalinowski J, Müller R, Luzhetskyy A. Perquinolines A-C: Unprecedented Bacterial Tetrahydroisoquinolines Involving an Intriguing Biosynthesis. Angew Chem Int Ed Engl 2019; 58:12930-12934. [PMID: 31310031 DOI: 10.1002/anie.201905538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Indexed: 01/15/2023]
Abstract
Metabolic profiling of Streptomyces sp. IB2014/016-6 led to the identification of three new tetrahydroisoquinoline natural products, perquinolines A-C (1-3). Labelled precursor feeding studies and the cloning of the pqr biosynthetic gene cluster revealed that 1-3 are assembled by the action of several unusual enzymes. The biosynthesis starts with the condensation of succinyl-CoA and l-phenylalanine catalyzed by the amino-7-oxononanoate synthase-like enzyme PqrA, representing rare chemistry in natural product assembly. The second condensation and cyclization events are conducted by PqrG, an enzyme resembling an acyl-CoA ligase. Last, ATP-grasp RimK-type ligase PqrI completes the biosynthesis by transferring a γ-aminobutyric acid or β-alanine moiety. The discovered pathway represents a new route for assembling the tetrahydroisoquinoline cores of natural products.
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Affiliation(s)
- Yuriy Rebets
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Suvd Nadmid
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Constanze Paulus
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Jennifer Herrmann
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Christian Rückert
- Center for Biotechnology-CeBiTec, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology-CeBiTec, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany.,Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
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Abstract
Stereospecific generation of α-amino ketones from common α-amino acids is difficult to achieve, often employing superstoichiometric alkylating reagents and requiring multiple protecting group manipulations. In contrast, the α-oxoamine synthase protein family performs this transformation stereospecifically in a single step without the need for protecting groups. Herein, we detail the characterization of the 8-amino-7-oxononanoate synthase (AONS) domain of the four-domain polyketide-like synthase SxtA, which natively mediates the formation of the ethyl ketone derivative of arginine. The function of each of the four domains is elucidated, leading to a revised proposal for the initiation of saxitoxin biosynthesis, a potent neurotoxin. We also demonstrate the synthetic potential of SxtA AONS, which is applied to the synthesis of a panel of novel α-amino ketones.
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Affiliation(s)
- Stephanie W Chun
- Department of Chemistry, University of Michigan, 930 North University Ave, Ann Arbor, MI 48109-1055, USA
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109-2216, USA
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, 930 North University Ave, Ann Arbor, MI 48109-1055, USA
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109-2216, USA
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Fujiwara T, Harigae H. Molecular pathophysiology and genetic mutations in congenital sideroblastic anemia. Free Radic Biol Med 2019; 133:179-185. [PMID: 30098397 DOI: 10.1016/j.freeradbiomed.2018.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/02/2018] [Accepted: 08/04/2018] [Indexed: 01/19/2023]
Abstract
Sideroblastic anemia is a heterogeneous congenital and acquired disorder characterized by anemia and the presence of ring sideroblasts in the bone marrow. Congenital sideroblastic anemia (CSA) is a rare disease caused by mutations in genes involved in the heme biosynthesis, iron-sulfur [Fe-S] cluster biosynthesis, and mitochondrial protein synthesis. The most prevalent form of CSA is X-linked sideroblastic anemia, caused by mutations in the erythroid-specific δ-aminolevulinate synthase (ALAS2), which is the first enzyme of the heme biosynthesis pathway in erythroid cells. To date, a remarkable number of genetically undefined CSA cases remain, but a recent application of the next-generation sequencing technology has recognized novel causative genes for CSA. However, in most instances, the detailed molecular mechanisms of how defects of each gene result in the abnormal mitochondrial iron accumulation remain unclear. This review aims to cover the current understanding of the molecular pathophysiology of CSA.
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Affiliation(s)
- Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575, Japan
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575, Japan.
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42
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Activated glycine receptors may decrease endosomal NADPH oxidase activity by opposing ClC-3-mediated efflux of chloride from endosomes. Med Hypotheses 2019; 123:125-129. [DOI: 10.1016/j.mehy.2019.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/15/2019] [Indexed: 12/25/2022]
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43
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Molecular expression, characterization and mechanism of ALAS2 gain-of-function mutants. Mol Med 2019; 25:4. [PMID: 30678654 PMCID: PMC6344999 DOI: 10.1186/s10020-019-0070-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/02/2019] [Indexed: 11/13/2022] Open
Abstract
Background X-linked protoporphyria (XLP) (MIM 300752) is an erythropoietic porphyria due to gain-of-function mutations in the last exon (Ducamp et al., Hum Mol Genet 22:1280-88, 2013) of the erythroid-specific aminolevulinate synthase gene (ALAS2). Five ALAS2 exon 11 variants identified by the NHBLI Exome sequencing project (p.R559H, p.E565D, p.R572C, p.S573F and p.Y586F) were expressed, purified and characterized in order to assess their possible contribution to XLP. To further characterize the XLP gain-of-function region, five novel ALAS2 truncation mutations (p.P561X, p.V562X, p.H563X, p.E569X and p.F575X) were also expressed and studied. Methods Site-directed mutagenesis was used to generate ALAS2 mutant clones and all were prokaryotically expressed, purified to near homogeneity and characterized by protein and enzyme kinetic assays. Standard deviations were calculated for 3 or more assay replicates. Results The five ALAS2 single nucleotide variants had from 1.3- to 1.9-fold increases in succinyl-CoA Vmax and 2- to 3-fold increases in thermostability suggesting that most could be gain-of-function modifiers of porphyria instead of causes. One SNP (p.R559H) had markedly low purification yield indicating enzyme instability as the likely cause for XLSA in an elderly patient with x-linked sideroblastic anemia. The five novel ALAS2 truncation mutations had increased Vmax values for both succinyl-CoA and glycine substrates (1.4 to 5.6-fold over wild-type), while the Kms for both substrates were only modestly changed. Of interest, the thermostabilities of the truncated ALAS2 mutants were significantly lower than wild-type, with an inverse relationship to Vmax fold-increase. Conclusions Patients with porphyrias should always be assessed for the presence of the ALAS2 gain-of-function modifier variants identified here. A key region of the ALAS2 carboxyterminal region is identified by the truncation mutations studied here and the correlation of increased thermolability with activity suggests that increased molecular flexibility/active site openness is the mechanism of enhanced function of mutations in this region providing further insights into the role of the carboxyl-terminal region of ALAS2 in the regulation of erythroid heme synthesis. Electronic supplementary material The online version of this article (10.1186/s10020-019-0070-9) contains supplementary material, which is available to authorized users.
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Ducamp S, Fleming MD. The molecular genetics of sideroblastic anemia. Blood 2019; 133:59-69. [PMID: 30401706 PMCID: PMC6318428 DOI: 10.1182/blood-2018-08-815951] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/21/2018] [Indexed: 01/19/2023] Open
Abstract
The sideroblastic anemias (SAs) are a group of inherited and acquired bone marrow disorders defined by pathological iron accumulation in the mitochondria of erythroid precursors. Like most hematological diseases, the molecular genetic basis of the SAs has ridden the wave of technology advancement. Within the last 30 years, with the advent of positional cloning, the human genome project, solid-state genotyping technologies, and next-generation sequencing have evolved to the point where more than two-thirds of congenital SA cases, and an even greater proportion of cases of acquired clonal disease, can be attributed to mutations in a specific gene or genes. This review focuses on an analysis of the genetics of these diseases and how understanding these defects may contribute to the design and implementation of rational therapies.
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Affiliation(s)
- Sarah Ducamp
- Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA
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45
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Tan Z, Zhao J, Chen J, Rao D, Zhou W, Chen N, Zheng P, Sun J, Ma Y. Enhancing thermostability and removing hemin inhibition of Rhodopseudomonas palustris 5-aminolevulinic acid synthase by computer-aided rational design. Biotechnol Lett 2018; 41:181-191. [PMID: 30498972 DOI: 10.1007/s10529-018-2627-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 11/17/2018] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To enhance the thermostability and deregulate the hemin inhibition of 5-aminolevulinic acid (ALA) synthase from Rhodopseudomonas palustris (RP-ALAS) by a computer-aided rational design strategy. RESULTS Eighteen RP-ALAS single variants were rationally designed and screened by measuring their residual activities upon heating. Among them, H29R and H15K exhibited a 2.3 °C and 6.0 °C higher melting temperature than wild-type, respectively. A 6.7-fold and 10.3-fold increase in specific activity after 1 h incubation at 37 °C was obtained for H29R (2.0 U/mg) and H15K (3.1 U/mg) compared to wild-type (0.3 U/mg). Additionally, higher residual activities in the presence of hemin were obtained for H29R and H15K (e.g., 64% and 76% at 10 μM hemin vs. 27% for wild-type). The ALA titer was increased by 6% and 22% in fermentation using Corynebacterium glutamicum ATCC 13032 expressing H29R and H15K, respectively. CONCLUSION H29R and H15K showed high thermostability, reduced hemin inhibition and slightly high activity, indicating that these two variants are good candidates for bioproduction of ALA.
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Affiliation(s)
- Zijian Tan
- College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin, 300457, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jing Zhao
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Deming Rao
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wenjuan Zhou
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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46
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Wilson RE, Menning DM, Wedemeyer K, Talbot SL. A transcriptome resource for the Arctic Cod (Boreogadus saida). Mar Genomics 2018. [DOI: 10.1016/j.margen.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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47
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Stoian N, Kaganjo J, Zeilstra-Ryalls J. Resolving the roles of the Rhodobacter sphaeroides HemA and HemT 5-aminolevulinic acid synthases. Mol Microbiol 2018; 110:1011-1029. [PMID: 30232811 DOI: 10.1111/mmi.14133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 11/30/2022]
Abstract
Strains of the phototrophic alpha-proteobacterium Rhodobacter sphaeroides vary in the number of enzymes catalyzing the formation of 5-aminolevulinic acid (ALA synthases) that are encoded in their genomes. All have hemA, but not all have hemT. This study compared transcription of these genes, and also properties of their products among three wild-type strains; 2.4.3 has hemA alone, 2.4.1 and 2.4.9 have both hemA and hemT. Using lacZ reporter plasmids all hemA genes were found to be upregulated under anaerobic conditions, but induction amplitudes differ. hemT is transcriptionally silent in 2.4.1 but actively transcribed in 2.4.9, and strongly upregulated under anaerobic-dark growth conditions when cells are respiring dimethyl sulfoxide, vs. aerobic-dark or phototrophic (anaerobic-light) conditions. Two extracytoplasmic function (ECF)-type sigma factors present in 2.4.9, but absent from 2.4.1 are directly involved in hemT transcription. Kinetic properties of the ALA synthases of all three strains were similar, but HemT enzymes are far less sensitive to feedback inhibition by hemin than HemA enzymes, and HemT is less active under oxidizing conditions. A model is presented that compares and contrast events in strains 2.4.1 and 2.4.9.
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Affiliation(s)
- Natalie Stoian
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - James Kaganjo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Jill Zeilstra-Ryalls
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
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48
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Ikushiro H, Nagami A, Takai T, Sawai T, Shimeno Y, Hori H, Miyahara I, Kamiya N, Yano T. Heme-dependent Inactivation of 5-Aminolevulinate Synthase from Caulobacter crescentus. Sci Rep 2018; 8:14228. [PMID: 30242198 PMCID: PMC6154995 DOI: 10.1038/s41598-018-32591-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/11/2018] [Indexed: 11/09/2022] Open
Abstract
The biosynthesis of heme is strictly regulated, probably because of the toxic effects of excess heme and its biosynthetic precursors. In many organisms, heme biosynthesis starts with the production of 5-aminolevulinic acid (ALA) from glycine and succinyl-coenzyme A, a process catalyzed by a homodimeric enzyme, pyridoxal 5′-phosphate (PLP)-dependent 5-aminolevulinate synthase (ALAS). ALAS activity is negatively regulated by heme in various ways, such as the repression of ALAS gene expression, degradation of ALAS mRNA, and inhibition of mitochondrial translocation of the mammalian precursor protein. There has been no clear evidence, however, that heme directly binds to ALAS to negatively regulate its activity. We found that recombinant ALAS from Caulobacter crescentus was inactivated via a heme-mediated feedback manner, in which the essential coenzyme PLP was rel eased to form the inactive heme-bound enzyme. The spectroscopic properties of the heme-bound ALAS showed that a histidine-thiolate hexa-coordinated ferric heme bound to each subunit with a one-to-one stoichiometry. His340 and Cys398 were identified as the axial ligands of heme, and mutant ALASs lacking either of these ligands became resistant to heme-mediated inhibition. ALAS expressed in C. crescentus was also found to bind heme, suggesting that heme-mediated feedback inhibition of ALAS is physiologically relevant in C. crescentus.
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Affiliation(s)
- Hiroko Ikushiro
- Department of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, 569-8686, Japan.
| | - Atsushi Nagami
- Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan
| | - Tomoko Takai
- Department of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, 569-8686, Japan.,Division of Diabetes and Endocrinology, Kobe University Graduate School of Medicine, Kobe, 650-0017, Japan
| | - Taiki Sawai
- Department of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, 569-8686, Japan
| | - Yuki Shimeno
- Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan
| | - Hiroshi Hori
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Ikuko Miyahara
- Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan
| | - Nobuo Kamiya
- Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, 558-8585, Japan
| | - Takato Yano
- Department of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, 569-8686, Japan.
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49
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Anti-Correlation between the Dynamics of the Active Site Loop and C-Terminal Tail in Relation to the Homodimer Asymmetry of the Mouse Erythroid 5-Aminolevulinate Synthase. Int J Mol Sci 2018; 19:ijms19071899. [PMID: 29958424 PMCID: PMC6073955 DOI: 10.3390/ijms19071899] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 11/17/2022] Open
Abstract
Biosynthesis of heme represents a complex process that involves multiple stages controlled by different enzymes. The first of these proteins is a pyridoxal 5′-phosphate (PLP)-dependent homodimeric enzyme, 5-aminolevulinate synthase (ALAS), that catalyzes the rate-limiting step in heme biosynthesis, the condensation of glycine with succinyl-CoA. Genetic mutations in human erythroid-specific ALAS (ALAS2) are associated with two inherited blood disorders, X-linked sideroblastic anemia (XLSA) and X-linked protoporphyria (XLPP). XLSA is caused by diminished ALAS2 activity leading to decreased ALA and heme syntheses and ultimately ineffective erythropoiesis, whereas XLPP results from “gain-of-function” ALAS2 mutations and consequent overproduction of protoporphyrin IX and increase in Zn2+-protoporphyrin levels. All XLPP-linked mutations affect the intrinsically disordered C-terminal tail of ALAS2. Our earlier molecular dynamics (MD) simulation-based analysis showed that the activity of ALAS2 could be regulated by the conformational flexibility of the active site loop whose structural features and dynamics could be changed due to mutations. We also revealed that the dynamic behavior of the two protomers of the ALAS2 dimer differed. However, how the structural dynamics of ALAS2 active site loop and C-terminal tail dynamics are related to each other and contribute to the homodimer asymmetry remained unanswered questions. In this study, we used bioinformatics and computational biology tools to evaluate the role(s) of the C-terminal tail dynamics in the structure and conformational dynamics of the murine ALAS2 homodimer active site loop. To assess the structural correlation between these two regions, we analyzed their structural displacements and determined their degree of correlation. Here, we report that the dynamics of ALAS2 active site loop is anti-correlated with the dynamics of the C-terminal tail and that this anti-correlation can represent a molecular basis for the functional and dynamic asymmetry of the ALAS2 homodimer.
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50
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Brown BL, Kardon JR, Sauer RT, Baker TA. Structure of the Mitochondrial Aminolevulinic Acid Synthase, a Key Heme Biosynthetic Enzyme. Structure 2018; 26:580-589.e4. [PMID: 29551290 DOI: 10.1016/j.str.2018.02.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/30/2017] [Accepted: 02/09/2018] [Indexed: 01/19/2023]
Abstract
5-Aminolevulinic acid synthase (ALAS) catalyzes the first step in heme biosynthesis. We present the crystal structure of a eukaryotic ALAS from Saccharomyces cerevisiae. In this homodimeric structure, one ALAS subunit contains covalently bound cofactor, pyridoxal 5'-phosphate (PLP), whereas the second is PLP free. Comparison between the subunits reveals PLP-coupled reordering of the active site and of additional regions to achieve the active conformation of the enzyme. The eukaryotic C-terminal extension, a region altered in multiple human disease alleles, wraps around the dimer and contacts active-site-proximal residues. Mutational analysis demonstrates that this C-terminal region that engages the active site is important for ALAS activity. Our discovery of structural elements that change conformation upon PLP binding and of direct contact between the C-terminal extension and the active site thus provides a structural basis for investigation of disruptions in the first step of heme biosynthesis and resulting human disorders.
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Affiliation(s)
- Breann L Brown
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia R Kardon
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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