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Nakamichi Y, Kobayashi J, Toyoda K, Suda M, Hiraga K, Inui M, Watanabe M. Structural basis for the allosteric pathway of 4-amino-4-deoxychorismate synthase. Acta Crystallogr D Struct Biol 2023; 79:895-908. [PMID: 37712435 DOI: 10.1107/s2059798323006320] [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: 03/13/2023] [Accepted: 07/20/2023] [Indexed: 09/16/2023] Open
Abstract
4-Amino-4-deoxychorismate synthase (ADCS), a chorismate-utilizing enzyme, is composed of two subunits: PabA and PabB. PabA is a glutamine amidotransferase that hydrolyzes glutamine into glutamate and ammonia. PabB is an aminodeoxychorismate synthase that converts chorismate to 4-amino-4-deoxychorismate (ADC) using the ammonia produced by PabA. ADCS functions under allosteric regulation between PabA and PabB. However, the allosteric mechanism remains unresolved because the structure of the PabA-PabB complex has not been determined. Here, the crystal structure and characterization of PapA from Streptomyces venezuelae (SvPapA), a bifunctional enzyme comprising the PabA and PabB domains, is reported. SvPapA forms a unique dimer in which PabA and PabB domains from different monomers complement each other and form an active structure. The chorismate-bound structure revealed that recognition of the C1 carboxyl group by Thr501 and Gly502 of the 498-PIKTG-502 motif in the PabB domain is essential for the catalytic Lys500 to reach the C2 atom, a reaction-initiation site. SvPapA demonstrated ADCS activity in the presence of Mg2+ when glutamate or NH+4 was used as the amino donor. The crystal structure indicated that the Mg2+-binding position changed depending on the binding of chorismate. In addition, significant structural changes were observed in the PabA domain depending on the presence or absence of chorismate. This study provides insights into the structural factors that are involved in the allosteric regulation of ADCS.
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Affiliation(s)
- Yusuke Nakamichi
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Jyumpei Kobayashi
- Research Institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Koichi Toyoda
- Research Institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Masako Suda
- Research Institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Kazumi Hiraga
- Research Institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Masahiro Watanabe
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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Lespinats S, De Clerck O, Colange B, Gorelova V, Grando D, Maréchal E, Van Der Straeten D, Rébeillé F, Bastien O. Phylogeny and Sequence Space: A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins. The Case Study of Aminodeoxychorismate Synthase. Acta Biotheor 2020; 68:139-156. [PMID: 31312977 DOI: 10.1007/s10441-019-09352-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/10/2019] [Indexed: 11/27/2022]
Abstract
During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylogenetic analysis tools, it is possible to study the evolutionary trajectories of proteins in the sequence space. Using the data-driven high-dimensional scaling method, we show that it is possible to predict and represent potential evolutionary trajectories by representing phylogenetic trees into a 3D projection of the sequence space. With the case of the aminodeoxychorismate synthase, an enzyme involved in folate synthesis, we show that this representation raises interesting questions about the complexity of the evolution of a given biological function, in particular concerning its capacity to explore the sequence space.
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Affiliation(s)
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Benoît Colange
- Univ. Grenoble Alpes, INES, 73375, Le Bourget du Lac, France
| | - Vera Gorelova
- Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium
- Department of Botany and Plant Biology, Laboratory of Plant Biochemistry and Physiology, University of Geneva, Quai E. Ansermet 30, 1211, Geneva, Switzerland
| | - Delphine Grando
- Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France
| | - Eric Maréchal
- Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France
| | - Dominique Van Der Straeten
- Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Fabrice Rébeillé
- Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France
| | - Olivier Bastien
- Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France.
- Laboratoire de Physiologie Cellulaire Végétale, Département Réponse et Dynamique Cellulaire, CEA Grenoble, UMR 5168, CNRS-CEA-INRA-Université J. Fourier, 17 rue des Martyrs, 38054, Grenoble Cedex 09, France.
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Gorelova V, Bastien O, De Clerck O, Lespinats S, Rébeillé F, Van Der Straeten D. Evolution of folate biosynthesis and metabolism across algae and land plant lineages. Sci Rep 2019; 9:5731. [PMID: 30952916 PMCID: PMC6451014 DOI: 10.1038/s41598-019-42146-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/25/2019] [Indexed: 11/09/2022] Open
Abstract
Tetrahydrofolate and its derivatives, commonly known as folates, are essential for almost all living organisms. Besides acting as one-carbon donors and acceptors in reactions producing various important biomolecules such as nucleic and amino acids, as well as pantothenate, they also supply one-carbon units for methylation reactions. Plants along with bacteria, yeast and fungi synthesize folates de novo and therefore constitute a very important dietary source of folates for animals. All the major steps of folate biosynthesis and metabolism have been identified but only few have been genetically characterized in a handful of model plant species. The possible differences in the folate pathway between various plant and algal species have never been explored. In this study we present a comprehensive comparative study of folate biosynthesis and metabolism of all major land plant lineages as well as green and red algae. The study identifies new features of plant folate metabolism that might open new directions to folate research in plants.
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Affiliation(s)
- V Gorelova
- Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium.,Department of Botany and Plant Biology, Laboratory of Plant Biochemistry and Physiology, University of Geneva, Quai E. Ansermet 30, 1211, Geneva, Switzerland
| | - O Bastien
- Laboratoire de Physiologie Cellulaire Vegetale, UMR168 CNRS-CEA-INRA-Universite Joseph Fourier Grenoble I, Bioscience and Biotechnologies Institute of Grenoble, CEA-Grenoble, 17 rue des Martyrs, 38054, Grenoble, Cedex 9, France
| | - O De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000, Gent, Belgium
| | - S Lespinats
- Laboratoire de Physiologie Cellulaire Vegetale, UMR168 CNRS-CEA-INRA-Universite Joseph Fourier Grenoble I, Bioscience and Biotechnologies Institute of Grenoble, CEA-Grenoble, 17 rue des Martyrs, 38054, Grenoble, Cedex 9, France
| | - F Rébeillé
- Laboratoire de Physiologie Cellulaire Vegetale, UMR168 CNRS-CEA-INRA-Universite Joseph Fourier Grenoble I, Bioscience and Biotechnologies Institute of Grenoble, CEA-Grenoble, 17 rue des Martyrs, 38054, Grenoble, Cedex 9, France
| | - D Van Der Straeten
- Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium.
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Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae. ISME JOURNAL 2018; 13:334-345. [PMID: 30228381 DOI: 10.1038/s41396-018-0274-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/30/2018] [Accepted: 07/27/2018] [Indexed: 11/09/2022]
Abstract
Ostreococcus tauri, a picoeukaryotic alga that contributes significantly to primary production in oligotrophic waters, has a highly streamlined genome, lacking the genetic capacity to grow without the vitamins thiamine (B1) and cobalamin (B12). Here we demonstrate that the B12 and B1 auxotrophy of O. tauri can be alleviated by co-culturing with a heterotrophic bacterial partner Dinoroseobacter shibae, a member of the Rhodobacteraceae family of alpha-proteobacteria, genera of which are frequently found associated with marine algae. D. shibae lacks the complete pathway to synthesise three other B-vitamins: niacin (B3), biotin (B7), and p-aminobenzoic acid (a precursor for folate, B9), and the alga is in turn able to satisfy the reciprocal vitamin requirements of its bacterial partner in a stable long-term co-culture. Bioinformatics searches of 197 representative marine bacteria with sequenced genomes identified just nine species that had a similar combination of traits (ability to make vitamin B12, but missing one or more genes for niacin and biotin biosynthesis enzymes), all of which were from the Rhodobacteraceae. Further analysis of 70 species from this family revealed the majority encoded the B12 pathway, but only half were able to make niacin, and fewer than 13% biotin. These characteristics may have either contributed to or resulted from the tendency of members of this lineage to adopt lifestyles in close association with algae. This study provides a nuanced view of bacterial-phytoplankton interactions, emphasising the complexity of the sources, sinks and dynamic cycling between marine microbes of these important organic micronutrients.
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Gorelova V, Ambach L, Rébeillé F, Stove C, Van Der Straeten D. Folates in Plants: Research Advances and Progress in Crop Biofortification. Front Chem 2017; 5:21. [PMID: 28424769 PMCID: PMC5372827 DOI: 10.3389/fchem.2017.00021] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/09/2017] [Indexed: 11/13/2022] Open
Abstract
Folates, also known as B9 vitamins, serve as donors and acceptors in one-carbon (C1) transfer reactions. The latter are involved in synthesis of many important biomolecules, such as amino acids, nucleic acids and vitamin B5. Folates also play a central role in the methyl cycle that provides one-carbon groups for methylation reactions. The important functions fulfilled by folates make them essential in all living organisms. Plants, being able to synthesize folates de novo, serve as an excellent dietary source of folates for animals that lack the respective biosynthetic pathway. Unfortunately, the most important staple crops such as rice, potato and maize are rather poor sources of folates. Insufficient folate consumption is known to cause severe developmental disorders in humans. Two approaches are employed to fight folate deficiency: pharmacological supplementation in the form of folate pills and biofortification of staple crops. As the former approach is considered rather costly for the major part of the world population, biofortification of staple crops is viewed as a decent alternative in the struggle against folate deficiency. Therefore, strategies, challenges and recent progress of folate enhancement in plants will be addressed in this review. Apart from the ever-growing need for the enhancement of nutritional quality of crops, the world population faces climate change catastrophes or environmental stresses, such as elevated temperatures, drought, salinity that severely affect growth and productivity of crops. Due to immense diversity of their biochemical functions, folates take part in virtually every aspect of plant physiology. Any disturbance to the plant folate metabolism leads to severe growth inhibition and, as a consequence, to a lower productivity. Whereas today's knowledge of folate biochemistry can be considered very profound, evidence on the physiological roles of folates in plants only starts to emerge. In the current review we will discuss the implication of folates in various aspects of plant physiology and development.
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Affiliation(s)
- Vera Gorelova
- Laboratory of Functional Plant Biology, Department of Biology, Ghent UniversityGhent, Belgium
| | - Lars Ambach
- Laboratory of Toxicology, Department of Bioanalysis, Ghent UniversityGhent, Belgium
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire Végétale, Bioscience and Biotechnologies Institute of Grenoble, CEA-GrenobleGrenoble, France
| | - Christophe Stove
- Laboratory of Toxicology, Department of Bioanalysis, Ghent UniversityGhent, Belgium
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Koma D, Yamanaka H, Moriyoshi K, Sakai K, Masuda T, Sato Y, Toida K, Ohmoto T. Production of P-aminobenzoic acid by metabolically engineered escherichia coli. Biosci Biotechnol Biochem 2014; 78:350-7. [PMID: 25036692 DOI: 10.1080/09168451.2014.878222] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The production of chemical compounds from renewable resources is an important issue in building a sustainable society. In this study, Escherichia coli was metabolically engineered by introducing T7lac promoter-controlled aroF(fbr), pabA, pabB, and pabC genes into the chromosome to overproduce para-aminobenzoic acid (PABA) from glucose. Elevating the copy number of chromosomal PT7lac-pabA-pabB distinctly increased the PABA titer, indicating that elevation of 4-amino-4-deoxychorismic acid synthesis is a significant factor in PABA production. The introduction of a counterpart derived from Corynebacterium efficiens, pabAB (ce), encoding a fused PabA and PabB protein, resulted in a considerable increase in the PABA titer. The introduction of more than two copies of PT7lac-pabAB (ce-mod), a codon-optimized pabAB (ce), into the chromosome of a strain that simultaneously overexpressed aroF(fbr) and pabC resulted in 5.1 mM PABA from 55.6 mM glucose (yield 9.2%). The generated strain produced 35 mM (4.8 g L(-1)) PABA from 167 mM glucose (yield 21.0%) in fed-batch culture.
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Affiliation(s)
- Daisuke Koma
- a Osaka Municipal Technical Research Institute , Osaka , Japan
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Camara D, Bisanz C, Barette C, Van Daele J, Human E, Barnard B, Van der Straeten D, Stove CP, Lambert WE, Douce R, Maréchal E, Birkholtz LM, Cesbron-Delauw MF, Dumas R, Rébeillé F. Inhibition of p-aminobenzoate and folate syntheses in plants and apicomplexan parasites by natural product rubreserine. J Biol Chem 2012; 287:22367-76. [PMID: 22577137 DOI: 10.1074/jbc.m112.365833] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Glutamine amidotransferase/aminodeoxychorismate synthase (GAT-ADCS) is a bifunctional enzyme involved in the synthesis of p-aminobenzoate, a central component part of folate cofactors. GAT-ADCS is found in eukaryotic organisms autonomous for folate biosynthesis, such as plants or parasites of the phylum Apicomplexa. Based on an automated screening to search for new inhibitors of folate biosynthesis, we found that rubreserine was able to inhibit the glutamine amidotransferase activity of the plant GAT-ADCS with an apparent IC(50) of about 8 μM. The growth rates of Arabidopsis thaliana, Toxoplasma gondii, and Plasmodium falciparum were inhibited by rubreserine with respective IC(50) values of 65, 20, and 1 μM. The correlation between folate biosynthesis and growth inhibition was studied with Arabidopsis and Toxoplasma. In both organisms, the folate content was decreased by 40-50% in the presence of rubreserine. In both organisms, the addition of p-aminobenzoate or 5-formyltetrahydrofolate in the external medium restored the growth for inhibitor concentrations up to the IC(50) value, indicating that, within this range of concentrations, rubreserine was specific for folate biosynthesis. Rubreserine appeared to be more efficient than sulfonamides, antifolate drugs known to inhibit the invasion and proliferation of T. gondii in human fibroblasts. Altogether, these results validate the use of the bifunctional GAT-ADCS as an efficient drug target in eukaryotic cells and indicate that the chemical structure of rubreserine presents interesting anti-parasitic (toxoplasmosis, malaria) potential.
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Affiliation(s)
- Djeneb Camara
- Laboratoire de Physiologie Cellulaire Végétale, Commissariat à l'Energie Atomique/CNRS UMR5168/INRA USC1200/Université Joseph Fourier Grenoble I, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France
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