1
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Stukey GJ, Han GS, Carman GM. Architecture and function of yeast phosphatidate phosphatase Pah1 domains/regions. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159547. [PMID: 39103045 DOI: 10.1016/j.bbalip.2024.159547] [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: 06/11/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
Phosphatidate (PA) phosphatase, which catalyzes the Mg2+-dependent dephosphorylation of PA to produce diacylglycerol, provides a direct precursor for the synthesis of the storage lipid triacylglycerol and the membrane phospholipids phosphatidylcholine and phosphatidylethanolamine. The enzyme controlling the key phospholipid PA also plays a crucial role in diverse aspects of lipid metabolism and cell physiology. PA phosphatase is a peripheral membrane enzyme that is composed of multiple domains/regions required for its catalytic function and subcellular localization. In this review, we discuss the domains/regions of PA phosphatase from the yeast Saccharomyces cerevisiae with reference to the homologous enzyme from mammalian cells.
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Affiliation(s)
- Geordan J Stukey
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA.
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2
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Paquay S, Duraffourd J, Bury M, Heremans IP, Caligiore F, Gerin I, Stroobant V, Jacobs J, Pinon A, Graff J, Vertommen D, Van Schaftingen E, Dewulf JP, Bommer GT. ACAD10 and ACAD11 allow entry of 4-hydroxy fatty acids into β-oxidation. Cell Mol Life Sci 2024; 81:367. [PMID: 39174697 PMCID: PMC11342911 DOI: 10.1007/s00018-024-05397-8] [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: 04/27/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/24/2024]
Abstract
Hydroxylated fatty acids are important intermediates in lipid metabolism and signaling. Surprisingly, the metabolism of 4-hydroxy fatty acids remains largely unexplored. We found that both ACAD10 and ACAD11 unite two enzymatic activities to introduce these metabolites into mitochondrial and peroxisomal β-oxidation, respectively. First, they phosphorylate 4-hydroxyacyl-CoAs via a kinase domain, followed by an elimination of the phosphate to form enoyl-CoAs catalyzed by an acyl-CoA dehydrogenase (ACAD) domain. Studies in knockout cell lines revealed that ACAD10 preferentially metabolizes shorter chain 4-hydroxy fatty acids than ACAD11 (i.e. 6 carbons versus 10 carbons). Yet, recombinant proteins showed comparable activity on the corresponding 4-hydroxyacyl-CoAs. This suggests that the localization of ACAD10 and ACAD11 to mitochondria and peroxisomes, respectively, might influence their physiological substrate spectrum. Interestingly, we observed that ACAD10 is cleaved internally during its maturation generating a C-terminal part consisting of the ACAD domain, and an N-terminal part comprising the kinase domain and a haloacid dehalogenase (HAD) domain. HAD domains often exhibit phosphatase activity, but negligible activity was observed in the case of ACAD10. Yet, inactivation of a presumptive key residue in this domain significantly increased the kinase activity, suggesting that this domain might have acquired a regulatory function to prevent accumulation of the phospho-hydroxyacyl-CoA intermediate. Taken together, our work reveals that 4-hydroxy fatty acids enter mitochondrial and peroxisomal fatty acid β-oxidation via two enzymes with an overlapping substrate repertoire.
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Affiliation(s)
- Stéphanie Paquay
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
- Department of Pediatric Neurology and Metabolic Diseases, Cliniques Universitaires St. Luc, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - Julia Duraffourd
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Marina Bury
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Isaac P Heremans
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Francesco Caligiore
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Isabelle Gerin
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | | | - Jean Jacobs
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Aymeric Pinon
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Julie Graff
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute & MASSPROT Platform, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - Emile Van Schaftingen
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Joseph P Dewulf
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
- Department of Laboratory Medicine, Cliniques Universitaires St. Luc, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - Guido T Bommer
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium.
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium.
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3
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Joyce AW, Searle BC. Computational approaches to identify sites of phosphorylation. Proteomics 2024; 24:e2300088. [PMID: 37897210 DOI: 10.1002/pmic.202300088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Due to their oftentimes ambiguous nature, phosphopeptide positional isomers can present challenges in bottom-up mass spectrometry-based workflows as search engine scores alone are often not enough to confidently distinguish them. Additional scoring algorithms can remedy this by providing confidence metrics in addition to these search results, reducing ambiguity. Here we describe challenges to interpreting phosphoproteomics data and review several different approaches to determine sites of phosphorylation for both data-dependent and data-independent acquisition-based workflows. Finally, we discuss open questions regarding neutral losses, gas-phase rearrangement, and false localization rate estimation experienced by both types of acquisition workflows and best practices for managing ambiguity in phosphosite determination.
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Affiliation(s)
- Alex W Joyce
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Brian C Searle
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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4
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Kaur H, Rode S, Kp S, Mahto JK, Alam MS, Gupta DN, Kar B, Singla J, Kumar P, Sharma AK. Characterization of haloacid dehalogenase superfamily acid phosphatase from Staphylococcus lugdunensis. Arch Biochem Biophys 2024; 753:109888. [PMID: 38232797 DOI: 10.1016/j.abb.2024.109888] [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: 11/10/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
The haloacid dehalogenase superfamily implicated in bacterial pathogenesis comprises different enzymes having roles in many metabolic pathways. Staphylococcus lugdunensis, a Gram-positive bacterium, is an opportunistic human pathogen causing infections in the central nervous system, urinary tract, bones, peritoneum, systemic conditions and cutaneous infection. The haloacid dehalogenase superfamily proteins play a significant role in the pathogenicity of certain bacteria, facilitating invasion, survival, and proliferation within host cells. The genome of S. lugdunensis encodes more than ten proteins belonging to this superfamily. However, none of them have been characterized. The present work reports the characterization of one of the haloacid dehalogenase superfamily proteins (SLHAD1) from Staphylococcus lugdunensis. The functional analysis revealed that SLHAD1 is a metal-dependent acid phosphatase, which catalyzes the dephosphorylation of phosphorylated metabolites of cellular pathways, including glycolysis, gluconeogenesis, nucleotides, and thiamine metabolism. Based on the substrate specificity and genomic analysis, the physiological function of SLHAD1 in thiamine metabolism has been tentatively assigned. The crystal structure of SLHAD1, lacking 49 residues at the C-terminal, was determined at 1.7 Å resolution with a homodimer in the asymmetric unit. It was observed that SLHAD1 exhibited time-dependent cleavage at a specific point, occurring through a self-initiated process. A combination of bioinformatics, biochemical, biophysical, and structural studies explored unique features of SLHAD1. Overall, the study revealed a detailed characterization of a critical enzyme of the human pathogen Staphylococcus lugdunensis, associated with several life-threatening infections.
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Affiliation(s)
- Harry Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Surabhi Rode
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Sandra Kp
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Jai Krishna Mahto
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Md Shahid Alam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Deena Nath Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Bibekananda Kar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Jitin Singla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India; Department of Computer Science and Engineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India.
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5
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Kinateder T, Mayer C, Nazet J, Sterner R. Improving enzyme functional annotation by integrating in vitro and in silico approaches: The example of histidinol phosphate phosphatases. Protein Sci 2024; 33:e4899. [PMID: 38284491 PMCID: PMC10804674 DOI: 10.1002/pro.4899] [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: 09/19/2023] [Revised: 12/13/2023] [Accepted: 01/01/2024] [Indexed: 01/30/2024]
Abstract
Advances in sequencing technologies have led to a rapid growth of public protein sequence databases, whereby the fraction of proteins with experimentally verified function continuously decreases. This problem is currently addressed by automated functional annotations with computational tools, which however lack the accuracy of experimental approaches and are susceptible to error propagation. Here, we present an approach that combines the efficiency of functional annotation by in silico methods with the rigor of enzyme characterization in vitro. First, a thorough experimental analysis of a representative enzyme of a group of homologues is performed which includes a focused alanine scan of the active site to determine a fingerprint of function-determining residues. In a second step, this fingerprint is used in combination with a sequence similarity network to identify putative isofunctional enzymes among the homologues. Using this approach in a proof-of-principle study, homologues of the histidinol phosphate phosphatase (HolPase) from Pseudomonas aeruginosa, many of which were annotated as phosphoserine phosphatases, were predicted to be HolPases. This functional annotation of the homologues was verified by in vitro testing of several representatives and an analysis of the occurrence of annotated HolPases in the corresponding phylogenetic groups. Moreover, the application of the same approach to the homologues of the HolPase from the archaeon Nitrosopumilus maritimus, which is not related to the HolPase from P. aeruginosa and was newly discovered in the course of this work, led to the annotation of the putative HolPase from various archaeal species.
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Affiliation(s)
- Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for BiochemistryUniversity of RegensburgRegensburgGermany
| | - Carina Mayer
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for BiochemistryUniversity of RegensburgRegensburgGermany
| | - Julian Nazet
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for BiochemistryUniversity of RegensburgRegensburgGermany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for BiochemistryUniversity of RegensburgRegensburgGermany
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6
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Sisodia R, Mazumdar PA, Madhurantakam C. In silico identification and analysis of potential inhibitors for acid phosphatase, HppA from Helicobacter pylori. J Mol Recognit 2023; 36:e3049. [PMID: 37553866 DOI: 10.1002/jmr.3049] [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: 03/30/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023]
Abstract
Helicobacter pylori is the most common cause of gastric ulcers and is associated with gastric cancer. The enzyme HppA of class C nonspecific acid phosphohydrolases (NSAPs) of H. pylori plays a crucial role in the electron transport chain. Herein, we report an in silico homology model of HppA consisting of a monomeric α + β model. A high throughput structure-based virtual screening approach yielded potential inhibitors against HppA with higher binding energies. Further analyses of molecular interaction maps and protein-ligand fingerprints, followed by molecular mechanics-generalized Born surface area (MM-GBSA) end point binding energy calculations of docked complexes, resulted in the detection of top binders/ligands. Our investigations identified potential substrate-competitive small molecule inhibitors of HppA, with admissible pharmacokinetic properties. These molecules may provide a starting point for developing novel therapeutic agents against H. pylori.
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Affiliation(s)
- Rinki Sisodia
- Structural and Molecular Biology Laboratory (SMBL), Department of Biotechnology, TERI School of Advanced Studies (TERI SAS), New Delhi, India
| | | | - Chaithanya Madhurantakam
- Structural and Molecular Biology Laboratory (SMBL), Department of Biotechnology, TERI School of Advanced Studies (TERI SAS), New Delhi, India
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7
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Zan X, Zhou Z, Wan J, Chen H, Zhu J, Xu H, Zhang J, Li X, Gao X, Chen R, Huang Z, Xu Z, Li L. Overexpression of OsHAD3, a Member of HAD Superfamily, Decreases Drought Tolerance of Rice. RICE (NEW YORK, N.Y.) 2023; 16:31. [PMID: 37468664 DOI: 10.1186/s12284-023-00647-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Haloacid dehalogenase-like hydrolase (HAD) superfamily have been shown to get involved in plant growth and abiotic stress response. Although the various functions and regulatory mechanism of HAD superfamily have been well demonstrated, we know little about the function of this family in conferring abiotic stress tolerance to rice. Here, we report OsHAD3, a HAD superfamily member, could affect drought tolerance of rice. Under drought stress, overexpression of OsHAD3 increases the accumulation of reactive oxygen species and malondialdehyde than wild type. OsHAD3-overexpression lines decreased but antisense-expression lines increased the roots length under drought stress and the transcription levels of many well-known stress-related genes were also changed in plants with different genotypes. Furthermore, overexpression of OsHAD3 also decreases the oxidative tolerance. Our results suggest that overexpression of OsHAD3 could decrease the drought tolerance of rice and provide a new strategy for improving drought tolerance in rice.
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Affiliation(s)
- Xiaofei Zan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Zhanmei Zhou
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Jiale Wan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Hao Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Jiali Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Haoran Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Jia Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Xiaohong Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Xiaoling Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China
| | - Rongjun Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China
| | - Zhengjian Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China
| | - Zhengjun Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China.
| | - Lihua Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China.
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8
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Youssef WA, Feil R, Saint-Sorny M, Johnson X, Lunn JE, Grimm B, Brzezowski P. Singlet oxygen-induced signalling depends on the metabolic status of the Chlamydomonas reinhardtii cell. Commun Biol 2023; 6:529. [PMID: 37193883 DOI: 10.1038/s42003-023-04872-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 04/24/2023] [Indexed: 05/18/2023] Open
Abstract
Using a mutant screen, we identified trehalose 6-phosphate phosphatase 1 (TSPP1) as a functional enzyme dephosphorylating trehalose 6-phosphate (Tre6P) to trehalose in Chlamydomonas reinhardtii. The tspp1 knock-out results in reprogramming of the cell metabolism via altered transcriptome. As a secondary effect, tspp1 also shows impairment in 1O2-induced chloroplast retrograde signalling. From transcriptomic analysis and metabolite profiling, we conclude that accumulation or deficiency of certain metabolites directly affect 1O2-signalling. 1O2-inducible GLUTATHIONE PEROXIDASE 5 (GPX5) gene expression is suppressed by increased content of fumarate and 2-oxoglutarate, intermediates in the tricarboxylic acid cycle (TCA cycle) in mitochondria and dicarboxylate metabolism in the cytosol, but also myo-inositol, involved in inositol phosphate metabolism and phosphatidylinositol signalling system. Application of another TCA cycle intermediate, aconitate, recovers 1O2-signalling and GPX5 expression in otherwise aconitate-deficient tspp1. Genes encoding known essential components of chloroplast-to-nucleus 1O2-signalling, PSBP2, MBS, and SAK1, show decreased transcript levels in tspp1, which also can be rescued by exogenous application of aconitate. We demonstrate that chloroplast retrograde signalling involving 1O2 depends on mitochondrial and cytosolic processes and that the metabolic status of the cell determines the response to 1O2.
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Affiliation(s)
- Waeil Al Youssef
- Pflanzenphysiologie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Maureen Saint-Sorny
- Photosynthesis and Environment Team, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), CNRS, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Aix-Marseille Université, UMR 7265, CEA Cadarache, F-13108, Saint-Paul-lez-Durance, France
| | - Xenie Johnson
- Photosynthesis and Environment Team, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), CNRS, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Aix-Marseille Université, UMR 7265, CEA Cadarache, F-13108, Saint-Paul-lez-Durance, France
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Bernhard Grimm
- Pflanzenphysiologie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Pawel Brzezowski
- Pflanzenphysiologie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
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Castro JC, Castro CG, Cobos M. Genetic and biochemical strategies for regulation of L-ascorbic acid biosynthesis in plants through the L-galactose pathway. FRONTIERS IN PLANT SCIENCE 2023; 14:1099829. [PMID: 37021310 PMCID: PMC10069634 DOI: 10.3389/fpls.2023.1099829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Vitamin C (L-ascorbic acid, AsA) is an essential compound with pleiotropic functions in many organisms. Since its isolation in the last century, AsA has attracted the attention of the scientific community, allowing the discovery of the L-galactose pathway, which is the main pathway for AsA biosynthesis in plants. Thus, the aim of this review is to analyze the genetic and biochemical strategies employed by plant cells for regulating AsA biosynthesis through the L-galactose pathway. In this pathway, participates eight enzymes encoded by the genes PMI, PMM, GMP, GME, GGP, GPP, GDH, and GLDH. All these genes and their encoded enzymes have been well characterized, demonstrating their participation in AsA biosynthesis. Also, have described some genetic and biochemical strategies that allow its regulation. The genetic strategy includes regulation at transcriptional and post-transcriptional levels. In the first one, it was demonstrated that the expression levels of the genes correlate directly with AsA content in the tissues/organs of the plants. Also, it was proved that these genes are light-induced because they have light-responsive promoter motifs (e.g., ATC, I-box, GT1 motif, etc.). In addition, were identified some transcription factors that function as activators (e.g., SlICE1, AtERF98, SlHZ24, etc.) or inactivators (e.g., SlL1L4, ABI4, SlNYYA10) regulate the transcription of these genes. In the second one, it was proved that some genes have alternative splicing events and could be a mechanism to control AsA biosynthesis. Also, it was demonstrated that a conserved cis-acting upstream open reading frame (5'-uORF) located in the 5'-untranslated region of the GGP gene induces its post-transcriptional repression. Among the biochemical strategies discovered is the control of the enzyme levels (usually by decreasing their quantities), control of the enzyme catalytic activity (by increasing or decreasing its activity), feedback inhibition of some enzymes (GME and GGP), subcellular compartmentation of AsA, the metabolon assembly of the enzymes, and control of AsA biosynthesis by electron flow. Together, the construction of this basic knowledge has been establishing the foundations for generating genetically improved varieties of fruits and vegetables enriched with AsA, commonly used in animal and human feed.
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Affiliation(s)
- Juan C. Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Carlos G. Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Marianela Cobos
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
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10
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Santos-Merino M, Yun L, Ducat DC. Cyanobacteria as cell factories for the photosynthetic production of sucrose. Front Microbiol 2023; 14:1126032. [PMID: 36865782 PMCID: PMC9971976 DOI: 10.3389/fmicb.2023.1126032] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Biofuels and other biologically manufactured sustainable goods are growing in popularity and demand. Carbohydrate feedstocks required for industrial fermentation processes have traditionally been supplied by plant biomass, but the large quantities required to produce replacement commodity products may prevent the long-term feasibility of this approach without alternative strategies to produce sugar feedstocks. Cyanobacteria are under consideration as potential candidates for sustainable production of carbohydrate feedstocks, with potentially lower land and water requirements relative to plants. Several cyanobacterial strains have been genetically engineered to export significant quantities of sugars, especially sucrose. Sucrose is not only naturally synthesized and accumulated by cyanobacteria as a compatible solute to tolerate high salt environments, but also an easily fermentable disaccharide used by many heterotrophic bacteria as a carbon source. In this review, we provide a comprehensive summary of the current knowledge of the endogenous cyanobacterial sucrose synthesis and degradation pathways. We also summarize genetic modifications that have been found to increase sucrose production and secretion. Finally, we consider the current state of synthetic microbial consortia that rely on sugar-secreting cyanobacterial strains, which are co-cultivated alongside heterotrophic microbes able to directly convert the sugars into higher-value compounds (e.g., polyhydroxybutyrates, 3-hydroxypropionic acid, or dyes) in a single-pot reaction. We summarize recent advances reported in such cyanobacteria/heterotroph co-cultivation strategies and provide a perspective on future developments that are likely required to realize their bioindustrial potential.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Lisa Yun
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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11
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A thermophilic phosphatase from Methanothermobacter marburgensis and its application to in vitro biosynthesis. Enzyme Microb Technol 2022; 159:110067. [DOI: 10.1016/j.enzmictec.2022.110067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/13/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022]
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12
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Unidirectional mannitol synthesis of Acinetobacter baumannii MtlD is facilitated by the helix-loop-helix-mediated dimer formation. Proc Natl Acad Sci U S A 2022; 119:e2107994119. [PMID: 35363566 PMCID: PMC9168451 DOI: 10.1073/pnas.2107994119] [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: 11/18/2022] Open
Abstract
Mannitol biosynthesis is essential for Acinetobacter baumannii to cope with osmotic stress. Currently, only Pseudomonas putida, Acinetobacter baylyi, and A. baumannii are able to de novo synthesize mannitol by a structurally unique bifunctional mannitol-1-phosphate dehydrogenase/phosphatase (AbMtlD). The molecular mechanism of reduction and dephosphorylation of fructose-6-phosphate to mannitol is highly dependent on the substrate shuffling from one protomer to the other protomer by a unique helix–loop–helix domain–mediated dimer formation, thus ensuring unidirectional and efficient biosynthesis of mannitol. These observations support an evolutionary adaptation of AbMtlD by fusion of dehydrogenase and phosphatase domains to facilitate efficient unidirectional enzymatic production of mannitol, unifying regulatory control and minimizing the intracellular concentration of toxic mannitol-1-phosphate during salt stress. Persistence of Acinetobacter baumannii in environments with low water activity is largely attributed to the biosynthesis of compatible solutes. Mannitol is one of the key compatible solutes in A. baumannii, and it is synthesized by a bifunctional mannitol-1-phosphate dehydrogenase/phosphatase (AbMtlD). AbMtlD catalyzes the conversion of fructose-6-phosphate to mannitol in two consecutive steps. Here, we report the crystal structure of dimeric AbMtlD, constituting two protomers each with a dehydrogenase and phosphatase domain. A proper assembly of AbMtlD dimer is facilitated by an intersection comprising a unique helix–loop–helix (HLH) domain. Reduction and dephosphorylation catalysis of fructose-6-phosphate to mannitol is dependent on the transient dimerization of AbMtlD. AbMtlD presents as a monomer under lower ionic strength conditions and was found to be mainly dimeric under high-salt conditions. The AbMtlD catalytic efficiency was markedly increased by cross-linking the protomers at the intersected HLH domain via engineered disulfide bonds. Inactivation of the AbMtlD phosphatase domain results in an intracellular accumulation of mannitol-1-phosphate in A. baumannii, leading to bacterial growth impairment upon salt stress. Taken together, our findings demonstrate that salt-induced dimerization of the bifunctional AbMtlD increases catalytic dehydrogenase and phosphatase efficiency, resulting in unidirectional catalysis of mannitol production.
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13
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Venkatachalam K, Ettrich RH. Role of aspartic acid residues D87 and D89 in APS kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthase 1 and 2b: A commonality with phosphatases/kinases. Biochem Biophys Rep 2021; 28:101155. [PMID: 34712849 PMCID: PMC8528679 DOI: 10.1016/j.bbrep.2021.101155] [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: 06/25/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022] Open
Abstract
3'-phosphoadenosine 5'-phosphosulfate (PAPS) is synthesized in two steps by PAPS synthase (PAPSS). PAPSS is comprised of ATP sulfurylase (ATPS) and APS kinase (APSK) domain activities. ATPS combines inorganic sulfate with α-phosphoryl of ATP to form adenosine 5'-phosphosulfate (APS) and PPi. In the second step APS is phosphorylated at 3'-OH using another mole of ATP to form PAPS and ADP catalyzed by APSK. The transfer of gamma-phosphoryl from ATP onto 3'-OH requires Mg2 + and purported to involve residues D87GD89N. We report that mutation of either aspartic residue to alanine completely abolishes APSK activity in PAPS formation. PAPSS is an, unique enzyme that binds to four different nucleotides: ATP and APS on both ATPS and APSK domains and ADP and PAPS exclusively on the APSK domain. The thermodynamic binding and the catalytic interplay must be very tightly controlled to form the end-product PAPS in the forward direction. Though APS binds to ATPS and APSK, in ATPS domain, the APS is a product and for APSK it is a substrate. DGDN motif is absent in ATPS and present in APSK. Mutation of D87 and D89 did not hamper ATPS activity however abolished APSK activity severely. Thus, D87GD89N region is required for stabilization of Mg2+-ATP, in the process of splitting the γ-phosphoryl from ATP and transfer of γ-phosphoryl onto 3'-OH of APS to form PAPS a process that cannot be achieved by ATPS domain. In addition, gamma32P-ATP, trapped phosphoryl enzyme intermediate more with PAPSS2 than with PAPSS1. This suggests inherent active site residues could control novel catalytic differences. Molecular docking studies of hPAPSS1with ATP + Mg2+ and APS of wild type and mutants supports the experimental results.
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Affiliation(s)
- K.V. Venkatachalam
- College of Allopathic Medicine, Nova Southeastern University, Ft. Lauderdale, FL, 33328, USA
| | - Rudiger H. Ettrich
- College of Biomedical Sciences, Larkin University, Miami, FL, 33169, USA
- Faculty of Mathematics and Physics, Charles University, 121 16, Prague, Czech Republic
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14
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Liu YJ, Zhang T, Chen S, Cheng D, Wu C, Wang X, Duan D, Zhu L, Lou H, Gong Z, Wang XD, Ho MS, Duan S. The noncanonical role of the protease cathepsin D as a cofilin phosphatase. Cell Res 2021; 31:801-813. [PMID: 33514914 PMCID: PMC8249557 DOI: 10.1038/s41422-020-00454-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/16/2020] [Indexed: 01/30/2023] Open
Abstract
Cathepsin D (cathD) is traditionally regarded as a lysosomal protease that degrades substrates in acidic compartments. Here we report cathD plays an unconventional role as a cofilin phosphatase orchestrating actin remodeling. In neutral pH environments, the cathD precursor directly dephosphorylates and activates the actin-severing protein cofilin independent of its proteolytic activity, whereas mature cathD degrades cofilin in acidic pH conditions. During development, cathD complements the canonical cofilin phosphatase slingshot and regulates the morphogenesis of actin-based structures. Moreover, suppression of cathD phosphatase activity leads to defective actin organization and cytokinesis failure. Our findings identify cathD as a dual-function molecule, whose functional switch is regulated by environmental pH and its maturation state, and reveal a novel regulatory role of cathD in actin-based cellular processes.
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Affiliation(s)
- Yi-Jun Liu
- grid.13402.340000 0004 1759 700XDepartment of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China ,grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Ting Zhang
- grid.13402.340000 0004 1759 700XDepartment of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China ,grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Sicong Chen
- grid.412465.0Clinical Research Center, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China
| | - Daxiao Cheng
- grid.13402.340000 0004 1759 700XDepartment of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China ,grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Cunjin Wu
- grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Xingyue Wang
- grid.13402.340000 0004 1759 700XDepartment of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China ,grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Duo Duan
- grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Liya Zhu
- grid.13402.340000 0004 1759 700XDepartment of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China ,grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Huifang Lou
- grid.13402.340000 0004 1759 700XDepartment of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China ,grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Zhefeng Gong
- grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Xiao-Dong Wang
- grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China ,grid.13402.340000 0004 1759 700XDepartment of Psychiatry, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016 China
| | - Margaret S. Ho
- grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
| | - Shumin Duan
- grid.13402.340000 0004 1759 700XDepartment of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009 China ,grid.13402.340000 0004 1759 700XResearch Units for Emotion and Emotion Disorders, NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058 China
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15
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Zhang Y, Fang W, Raimi OG, Lockhart DEA, Ferenbach AT, Lu L, van Aalten DMF. Genetic and structural validation of phosphomannomutase as a cell wall target in Aspergillus fumigatus. Mol Microbiol 2021; 116:245-259. [PMID: 33629421 DOI: 10.1111/mmi.14706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 11/29/2022]
Abstract
Aspergillus fumigatus is an opportunistic mold responsible for severe life-threatening fungal infections in immunocompromised patients. The cell wall, an essential structure composed of glucan, chitin, and galactomannan, is considered to be a target for the development of antifungal drugs. The nucleotide sugar donor GDP-mannose (GDP-Man) is required for the biosynthesis of galactomannan, glycosylphosphatidylinositol (GPI) anchors, glycolipid, and protein glycosylation. Starting from fructose-6-phosphate, GDP-Man is produced by the sequential action of the enzymes phosphomannose isomerase, phosphomannomutase (Pmm), and GDP-mannose pyrophosphorylase. Here, using heterokaryon rescue and gene knockdown approaches we demonstrate that the phosphomannomutase encoding gene in A. fumigatus (pmmA) is essential for survival. Reduced expression of pmmA is associated with significant morphological defects including retarded germination, growth, reduced conidiation, and abnormal polarity. Moreover, the knockdown strain exhibited an altered cell wall organization and sensitivity toward cell wall perturbing agents. By solving the first crystal structure of A. fumigatus phosphomannomutase (AfPmmA) we identified non-conservative substitutions near the active site when compared to the human orthologues. Taken together, this work provides a genetic and structural foundation for the exploitation of AfPmmA as a potential antifungal target.
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Affiliation(s)
- Yuanwei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,School of Life Sciences, University of Dundee, Dundee, UK
| | - Wenxia Fang
- School of Life Sciences, University of Dundee, Dundee, UK.,National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | | | | | | | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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16
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Wang J, Singh SK, Geng S, Zhang S, Yuan L. Genome-wide analysis of glycerol-3-phosphate O-acyltransferase gene family and functional characterization of two cutin group GPATs in Brassica napus. PLANTA 2020; 251:93. [PMID: 32246349 DOI: 10.1007/s00425-020-03384-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Genome-wide identification, spatio-temporal expression analysis and functional characterization of selected Brassica napus GPATs highlight their roles in cuticular wax biosynthesis and defense against fungal pathogens. Glycerol-3-phosphate 1-O-acyltransferase (GPAT) is a key enzyme in the biosynthesis of glycerolipids, a major component of cellular membranes and extracellular protective layers, such as cuticles in plants. Brassica napus is an economically important crop and cultivated worldwide mostly for its edible oil. The B. napus GPATs (BnGPATs) are insufficiently characterized. Here, we performed genome-wide analysis to identify putative GPATs in B. napus and its diploid progenitors B. rapa and B oleracea. The 32 B. napus BnGPATs are phylogenetically divided into three major groups, cutin, suberin, and diverse ancient groups. Analysis of transcriptomes of different tissues and seeds at different developmental stages revealed the spatial and temporal expression profiles of BnGPATs. The yield and oil quality of B. napus are adversely affected by the necrotrophic fungus, Sclerotinia sclerotiorum. We showed that several BnGPATs, including cutin-related BnGPAT19 and 21, were upregulated in the S. sclerotiorum resistant line. RNAi-mediated suppression of BnGPAT19 and 21 in B. napus resulted in thinner cuticle, leading to rapid water and chlorophyll loss in toluidine blue staining and leaf bleaching assays. In addition, the RNAi plants also developed severe necrotic lesions following fungal inoculation compared to the wild-type plants, indicating that BnGPAT19 and 21 are likely involved in cuticular wax biosynthesis that is critical for initial pathogen defense. Taken together, we provided a comprehensive account of GPATs B. napus and characterized BnGPAT19 and 21 for their potential roles in cuticular wax biosynthesis and defense against fungal pathogens.
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Affiliation(s)
- Jingxue Wang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
| | - Sanjay Kumar Singh
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Siyu Geng
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Shanshan Zhang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Ling Yuan
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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17
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He Q, Toh JD, Ero R, Qiao Z, Kumar V, Serra A, Tan J, Sze SK, Gao YG. The unusual di-domain structure of Dunaliella salina glycerol-3-phosphate dehydrogenase enables direct conversion of dihydroxyacetone phosphate to glycerol. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:153-164. [PMID: 31762135 DOI: 10.1111/tpj.14619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/31/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Dunaliella has been extensively studied due to its intriguing adaptation to high salinity. Its di-domain glycerol-3-phosphate dehydrogenase (GPDH) isoform is likely to underlie the rapid production of the osmoprotectant glycerol. Here, we report the structure of the chimeric Dunaliella salina GPDH (DsGPDH) protein featuring a phosphoserine phosphatase-like domain fused to the canonical glycerol-3-phosphate (G3P) dehydrogenase domain. Biochemical assays confirm that DsGPDH can convert dihydroxyacetone phosphate (DHAP) directly to glycerol, whereas a separate phosphatase protein is required for this conversion process in most organisms. The structure of DsGPDH in complex with its substrate DHAP and co-factor nicotinamide adenine dinucleotide (NAD) allows the identification of the residues that form the active sites. Furthermore, the structure reveals an intriguing homotetramer form that likely contributes to the rapid biosynthesis of glycerol.
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Affiliation(s)
- Qinghua He
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, College of Life Science and Technology, Southwest Minzu University, Chengdu, 610041, China
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Joel Dewei Toh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore City, 138673, Singapore
| | - Rya Ero
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 639798, Singapore
| | - Zhu Qiao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 639798, Singapore
| | - Veerendra Kumar
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore City, 138673, Singapore
| | - Aida Serra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Jackie Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore City, 138673, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 639798, Singapore
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18
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PA0335, a Gene Encoding Histidinol Phosphate Phosphatase, Mediates Histidine Auxotrophy in Pseudomonas aeruginosa. Appl Environ Microbiol 2020; 86:AEM.02593-19. [PMID: 31862725 DOI: 10.1128/aem.02593-19] [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: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 11/20/2022] Open
Abstract
The biosynthesis of histidine, a proteinogenic amino acid, has been extensively studied due to its importance in bacterial growth and survival. Histidinol-phosphate phosphatase (Hol-Pase), which is responsible for the penultimate step of histidine biosynthesis, is generally the last enzyme to be characterized in many bacteria because its origin and evolution are more complex compared to other enzymes in histidine biosynthesis. However, none of the enzymes in histidine biosynthesis, including Hol-Pase, have been characterized in Pseudomonas aeruginosa, which is an important opportunistic Gram-negative pathogen that can cause serious human infections. In our previous work, a transposon mutant of P. aeruginosa was found to display a growth defect on glucose-containing minimal solid medium. In this study, we found that the growth defect was due to incomplete histidine auxotrophy caused by PA0335 inactivation. Subsequently, PA0335 was shown to encode Hol-Pase, and its function and enzymatic activity were investigated using genetic and biochemical methods. In addition to PA0335, the roles of 12 other predicted genes involved in histidine biosynthesis in P. aeruginosa were examined. Among them, hisC2 (PA3165), hisH2 (PA3152), and hisF2 (PA3151) were found to be dispensable for histidine synthesis, whereas hisG (PA4449), hisE (PA5067), hisF1 (PA5140), hisB (PA5143), hisI (PA5066), hisC1 (PA4447), and hisA (PA5141) were essential because deletion of each resulted in complete histidine auxotrophy; similar to the case for PA0335, hisH1 (PA5142) or hisD (PA4448) deletion caused incomplete histidine auxotrophy. Taken together, our results outline the histidine synthesis pathway of P. aeruginosa IMPORTANCE Histidine is a common amino acid in proteins. Because it plays critical roles in bacterial metabolism, its biosynthetic pathway in many bacteria has been elucidated. However, the pathway remains unclear in Pseudomonas aeruginosa, an important opportunistic pathogen in clinical settings; in particular, there is scant knowledge about histidinol-phosphate phosphatase (Hol-Pase), which has a complex origin and evolution. In this study, P. aeruginosa Hol-Pase was identified and characterized. Furthermore, the roles of all other predicted genes involved in histidine biosynthesis were examined. Our results illustrate the histidine synthesis pathway of P. aeruginosa The knowledge obtained from this study may help in developing strategies to control P. aeruginosa-related infections. In addition, some enzymes of the histidine synthesis pathway from P. aeruginosa might be used as elements of histidine synthetic biology in other industrial microorganisms.
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Zhang Z, van der Donk WA. Nonribosomal Peptide Extension by a Peptide Amino-Acyl tRNA Ligase. J Am Chem Soc 2019; 141:19625-19633. [PMID: 31751505 DOI: 10.1021/jacs.9b07111] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The catalytic use of a small peptide scaffold for the biosynthesis of amino acid-derived natural products is a recently discovered new biosynthetic strategy. During this process, a peptide-amino acyl tRNA ligase (PEARL) adds amino acids to the C-terminus of a small peptide scaffold in an ATP- and tRNA-dependent process. The mechanism of this unusual transformation is currently not known. In this study, we present a detailed biochemical and mechanistic study of TglB (UniProtKB-F3HQJ1), a PEARL that catalyzes the addition of Cys to the C-terminus of the peptide TglA in the biosynthesis of 3-thiaglutamate in the plant pathogen Pseudomonas syringae. TglB recognizes several important residues close to the C-terminus of TglA to perform its activity and is tolerant with respect to the last amino acid of its substrate peptide. The enzyme recognizes the acceptor stem of tRNACys, as micro- and minihelices, truncated versions of full-length tRNACys that contain the acceptor stem, were also accepted. Mutagenesis of conserved residues in TglB identified several key residues for catalysis and did not support the possibility of TglB adopting various ping-pong mechanisms to catalyze the amino acid addition reaction. Using isotopic labeling studies, we demonstrate that ATP is used to directly phosphorylate the C-terminal carboxylate of TglA. Collectively, the data support a general mechanism for the amino acid addition reaction catalyzed by this class of enzyme.
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Affiliation(s)
- Zhengan Zhang
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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20
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Park SM, Seo EH, Bae DH, Kim SS, Kim J, Lin W, Kim KH, Park JB, Kim YS, Yin J, Kim SY. Phosphoserine Phosphatase Promotes Lung Cancer Progression through the Dephosphorylation of IRS-1 and a Noncanonical L-Serine-Independent Pathway. Mol Cells 2019; 42:604-616. [PMID: 31446747 PMCID: PMC6715339 DOI: 10.14348/molcells.2019.0160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Phosphoserine phosphatase (PSPH) is one of the key enzymes of the L-serine synthesis pathway. PSPH is reported to affect the progression and survival of several cancers in an L-serine synthesis-independent manner, but the mechanism remains elusive. We demonstrate that PSPH promotes lung cancer progression through a noncanonical L-serine-independent pathway. PSPH was significantly associated with the prognosis of lung cancer patients and regulated the invasion and colony formation of lung cancer cells. Interestingly, L-serine had no effect on the altered invasion and colony formation by PSPH. Upon measuring the phosphatase activity of PSPH on a serine-phosphorylated peptide, we found that PSPH dephosphorylated phospho-serine in peptide sequences. To identify the target proteins of PSPH, we analyzed the protein phosphorylation profile and the PSPH-interacting protein profile using proteomic analyses and found one putative target protein, IRS-1. Immunoprecipitation and immunoblot assays validated a specific interaction between PSPH and IRS1 and the dephosphorylation of phospho-IRS-1 by PSPH in lung cancer cells. We suggest that the specific interaction and dephosphorylation activity of PSPH have novel therapeutic potential for lung cancer treatment, while the metabolic activity of PSPH, as a therapeutic target, is controversial.
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Affiliation(s)
- Seong-Min Park
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141,
Korea
- Research Institute, National Cancer Center, Goyang 10408,
Korea
| | - Eun-Hye Seo
- Genome Editing Research Center, KRIBB, Daejeon 34141,
Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113,
Korea
| | - Dong-Hyuck Bae
- Genome Editing Research Center, KRIBB, Daejeon 34141,
Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113,
Korea
| | - Sung Soo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408,
Korea
- Research Institute, National Cancer Center, Goyang 10408,
Korea
| | - Jina Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141,
Korea
- Genome Editing Research Center, KRIBB, Daejeon 34141,
Korea
| | - Weiwei Lin
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408,
Korea
- Research Institute, National Cancer Center, Goyang 10408,
Korea
| | - Kyung-Hee Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408,
Korea
- Research Institute, National Cancer Center, Goyang 10408,
Korea
| | - Jong Bae Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408,
Korea
- Research Institute, National Cancer Center, Goyang 10408,
Korea
| | - Yong Sung Kim
- Genome Editing Research Center, KRIBB, Daejeon 34141,
Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113,
Korea
| | - Jinlong Yin
- Henan and Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng 475004,
China
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408,
Korea
- Research Institute, National Cancer Center, Goyang 10408,
Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113,
Korea
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21
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Havlickova P, Brinsa V, Brynda J, Pachl P, Prudnikova T, Mesters JR, Kascakova B, Kuty M, Pusey ML, Ng JD, Rezacova P, Kuta Smatanova I. A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:743-752. [PMID: 31373573 DOI: 10.1107/s2059798319009586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/03/2019] [Indexed: 11/11/2022]
Abstract
The haloacid dehalogenase (HAD) superfamily is one of the largest known groups of enzymes and the majority of its members catalyze the hydrolysis of phosphoric acid monoesters into a phosphate ion and an alcohol. Despite the fact that sequence similarity between HAD phosphatases is generally very low, the members of the family possess some characteristic features, such as a Rossmann-like fold, HAD signature motifs or the requirement for Mg2+ ion as an obligatory cofactor. This study focuses on a new hypothetical HAD phosphatase from Thermococcus thioreducens. The protein crystallized in space group P21212, with unit-cell parameters a = 66.3, b = 117.0, c = 33.8 Å, and the crystals contained one molecule in the asymmetric unit. The protein structure was determined by X-ray crystallography and was refined to 1.75 Å resolution. The structure revealed a putative active site common to all HAD members. Computational docking into the crystal structure was used to propose substrates of the enzyme. The activity of this thermophilic enzyme towards several of the selected substrates was confirmed at temperatures of 37°C as well as 60°C.
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Affiliation(s)
- Petra Havlickova
- Institute of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 1760, CZ-370 05 Ceske Budejovice, Czech Republic
| | - Vitezslav Brinsa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, CZ-166 10 Prague, Czech Republic
| | - Jiri Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, CZ-166 10 Prague, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, CZ-166 10 Prague, Czech Republic
| | - Tatyana Prudnikova
- Institute of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 1760, CZ-370 05 Ceske Budejovice, Czech Republic
| | - Jeroen R Mesters
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Barbora Kascakova
- Institute of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 1760, CZ-370 05 Ceske Budejovice, Czech Republic
| | - Michal Kuty
- Institute of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 1760, CZ-370 05 Ceske Budejovice, Czech Republic
| | - Marc L Pusey
- Department of Biologial Sciences, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - Joseph D Ng
- Department of Biologial Sciences, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - Pavlina Rezacova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, CZ-166 10 Prague, Czech Republic
| | - Ivana Kuta Smatanova
- Institute of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 1760, CZ-370 05 Ceske Budejovice, Czech Republic
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22
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Wang W, Meng D, Li Q, Li Z, You C. Characterization of a hyperthermophilic phosphatase from Archaeoglobus fulgidus and its application in in vitro synthetic enzymatic biosystem. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0257-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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Meng D, Liang A, Wei X, You C. Enzymatic characterization of a thermostable phosphatase from Thermomicrobium roseum and its application for biosynthesis of fructose from maltodextrin. Appl Microbiol Biotechnol 2019; 103:6129-6139. [PMID: 31172205 DOI: 10.1007/s00253-019-09917-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 01/09/2023]
Abstract
Phosphatases, which catalyze the dephosphorylation of compounds containing phosphate groups, are important members of the haloacid dehalogenase (HAD)-like superfamily. Herein, a thermostable phosphatase encoded by an open reading frame of Trd_1070 from Thermomicrobium roseum was enzymologically characterized. This phosphatase showed promiscuous activity against more than ten sugar phosphates, with high specific activity toward ribose 5-phosphate, followed by ribulose 5-phosphate and fructose 6-phosphate. The half-life of Trd_1070 at 70 °C and pH 7.0 was about 14.2 h. Given that the catalytic efficiency of Trd_1070 on fructose 6-phosphate was 49-fold higher than that on glucose 6-phosphate, an in vitro synthetic biosystem containing alpha-glucan phosphorylase, phosphoglucomutase, phosphoglucose isomerase, and Trd_1070 was constructed for the production of fructose from maltodextrin by whole-cell catalysis, resulting in 21.6 g/L fructose with a ratio of fructose to glucose of approximately 2:1 from 50 g/L maltodextrin. This in vitro biosystem provides an alternative method to produce fructose with higher fructose content compared with the traditional production method using glucose isomerization. Further discovery and enzymologic characterization of phosphatases may promote further production of alternative monosaccharides through in vitro synthetic biosystems.
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Affiliation(s)
- Dongdong Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Ailing Liang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,School of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xinlei Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.
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24
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Haufroid M, Wouters J. Targeting the Serine Pathway: A Promising Approach against Tuberculosis? Pharmaceuticals (Basel) 2019; 12:E66. [PMID: 31052291 PMCID: PMC6630544 DOI: 10.3390/ph12020066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/22/2022] Open
Abstract
Tuberculosis is still the leading cause of death by a single infectious agent. Effective chemotherapy has been used and improved since the 1950s, but strains resistant to this therapy and most antibacterial drugs on the market are emerging. Only 10 new drugs are in clinical trials, and two of them have already demonstrated resistance. This paper gives an overview of current treatment options against tuberculosis and points out a promising approach of discovering new effective drugs. The serine production pathway is composed of three enzymes (SerA1, SerC and SerB2), which are considered essential for bacterial growth, and all of them are considered as a therapeutic drug target. Their crystal structure are described and essential regulatory domains pointed out. Sequence alignment with similar enzymes in other host would help to identify key residues to target in order to achieve selective inhibition. Currently, only inhibitors of SerB2 are described in the literature. However, inhibitors of human enzymes are discussed, and could be used as a good starting point for a drug discovery program. The aim of this paper is to give some guidance for the design of new hits for every enzyme in this pathway.
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Affiliation(s)
- Marie Haufroid
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Medicine and Drug Innovation Center (Namedic), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), B-5000 Namur, Belgium.
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Medicine and Drug Innovation Center (Namedic), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), B-5000 Namur, Belgium.
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25
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Effects of triethylamine on the expression patterns of two G3PDHs and lipid accumulation in Dunaliella tertiolecta. Enzyme Microb Technol 2019; 127:17-21. [PMID: 31088612 DOI: 10.1016/j.enzmictec.2019.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/20/2019] [Accepted: 04/04/2019] [Indexed: 12/17/2022]
Abstract
Glycerol-3-phosphate (G3P) is the important precursors for triacylglycerol synthesis, while glycerol-3-phosphate dehydrogenase (GPDH) determines the formation of G3P. In this study, two GDPH genes, Dtgdp1 and Dtgdp2 were isolated and identified from Dunaliella tertiolecta. The full-length Dtgdp1 and Dtgdp2 CDS were 2016 bp and 2094 bp, which encoded two putative protein sequences of 671 and 697 amino acids with predicted molecular weights of 73.64 kDa and 76.73 kDa, respectively. DtGDP1 and DtGDP2 both had a close relationship with those of algal and higher plants. DtGDP1 shared two conserved superfamily (A1 and A2) and four signature motifs (I-IV), and the DtGDP2 showed six signature domains (from motif I to VI) and DAO_C conserved family. Our previous work showed that the triethylamine intervention could greatly increase the triacylglycerol content (up to 80%) of D. tertiolecta. This study aims to investigate the effect of triethylamine on GPDH expression. Results showed that, when treated by triethylamine at 100 ppm and 150 ppm, the expression levels of Dtgdp1 and Dtgpd2 were increased to 5.121- and 56.964-fold compared with the control, respectively. Triethylamine seemed to enhance lipid metabolic flow by inducing the expressions of Dtgdp1 and Dtgdp2 to increase the lipid content, which provides a new insight into the desired pathway of lipid synthesis in algae through genetic engineering.
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26
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Hennessy M, Granade ME, Hassaninasab A, Wang D, Kwiatek JM, Han GS, Harris TE, Carman GM. Casein kinase II-mediated phosphorylation of lipin 1β phosphatidate phosphatase at Ser-285 and Ser-287 regulates its interaction with 14-3-3β protein. J Biol Chem 2019; 294:2365-2374. [PMID: 30617183 DOI: 10.1074/jbc.ra118.007246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/04/2019] [Indexed: 12/20/2022] Open
Abstract
The mammalian lipin 1 phosphatidate phosphatase is a key regulatory enzyme in lipid metabolism. By catalyzing phosphatidate dephosphorylation, which produces diacylglycerol, the enzyme plays a major role in the synthesis of triacylglycerol and membrane phospholipids. The importance of lipin 1 to lipid metabolism is exemplified by cellular defects and lipid-based diseases associated with its loss or overexpression. Phosphorylation of lipin 1 governs whether it is associated with the cytoplasm apart from its substrate or with the endoplasmic reticulum membrane where its enzyme reaction occurs. Lipin 1β is phosphorylated on multiple sites, but less than 10% of them are ascribed to a specific protein kinase. Here, we demonstrate that lipin 1β is a bona fide substrate for casein kinase II (CKII), a protein kinase that is essential to viability and cell cycle progression. Phosphoamino acid analysis and phosphopeptide mapping revealed that lipin 1β is phosphorylated by CKII on multiple serine and threonine residues, with the former being major sites. Mutational analysis of lipin 1β and its peptides indicated that Ser-285 and Ser-287 are both phosphorylated by CKII. Substitutions of Ser-285 and Ser-287 with nonphosphorylatable alanine attenuated the interaction of lipin 1β with 14-3-3β protein, a regulatory hub that facilitates the cytoplasmic localization of phosphorylated lipin 1. These findings advance our understanding of how phosphorylation of lipin 1β phosphatidate phosphatase regulates its interaction with 14-3-3β protein and intracellular localization and uncover a mechanism by which CKII regulates cellular physiology.
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Affiliation(s)
- Meagan Hennessy
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
| | - Mitchell E Granade
- the Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908
| | - Azam Hassaninasab
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
| | - Dana Wang
- the Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908
| | - Joanna M Kwiatek
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
| | - Gil-Soo Han
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
| | - Thurl E Harris
- the Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908
| | - George M Carman
- From the Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
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27
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Crystallization of Liganded Phosphatases in the HAD Superfamily. Methods Enzymol 2018; 607:157-184. [PMID: 30149857 DOI: 10.1016/bs.mie.2018.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phosphotransferases catalyze reactions on chemically diverse molecules in organisms from all domains of life. The haloalkanoate dehalogenase superfamily (HADSF) is a model system for phosphoryl transfer enzymes as members catalyze phosphoester hydrolase, phosphonate hydrolase, and phosphomutase reactions on sugars, lipids, nucleotides, and peptides. Because these reactions are fundamental to essential metabolic transformations, understanding the mechanism and determinants of substrate specificity in the HADSF is critical. Structure/function relationships in the superfamily have also been leveraged in the development of methodologies for the assignment of enzyme function. Enzyme complexes with substrate, product, and analogs of the ground state or intermediate/transition state can be studied via high-resolution macromolecular crystallography to provide insight to the relative location of residues and ligands, as well as associated enzyme conformational states. This knowledge can aid in inhibitor design for phosphohydrolase reactions and target-specific therapeutics. Here we describe experimental approaches to capture liganded X-ray crystallographic structures of HADSF members. A number of these methods can be employed generally, including other families of phosphohydrolases and enzymes catalyzing phosphoryl transfer.
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28
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Dieck CL, Tzoneva G, Forouhar F, Carpenter Z, Ambesi-Impiombato A, Sánchez-Martín M, Kirschner-Schwabe R, Lew S, Seetharaman J, Tong L, Ferrando AA. Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Cancer Cell 2018; 34:136-147.e6. [PMID: 29990496 PMCID: PMC6049837 DOI: 10.1016/j.ccell.2018.06.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/06/2018] [Accepted: 06/06/2018] [Indexed: 11/25/2022]
Abstract
Activating mutations in the cytosolic 5'-nucleotidase II gene NT5C2 drive resistance to 6-mercaptopurine in acute lymphoblastic leukemia. Here we demonstrate that constitutively active NT5C2 mutations K359Q and L375F reconfigure the catalytic center for substrate access and catalysis in the absence of allosteric activator. In contrast, most relapse-associated mutations, which involve the arm segment and residues along the surface of the inter-monomeric cavity, disrupt a built-in switch-off mechanism responsible for turning off NT5C2. In addition, we show that the C-terminal acidic tail lost in the Q523X mutation functions to restrain NT5C2 activation. These results uncover dynamic mechanisms of enzyme regulation targeted by chemotherapy resistance-driving NT5C2 mutations, with important implications for the development of NT5C2 inhibitor therapies.
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Affiliation(s)
- Chelsea L Dieck
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Gannie Tzoneva
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Farhad Forouhar
- Hervert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA; Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA
| | - Zachary Carpenter
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | | | | | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Scott Lew
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA
| | | | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA.
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University Medical Center, 1130 St. Nicholas Avenue, ICRC 402, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
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29
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Jin T, Gao Y, He K, Ge F. Expression Profiles of the Trehalose-6-Phosphate Synthase Gene Associated With Thermal Stress in Ostrinia furnacalis (Lepidoptera: Crambidae). JOURNAL OF INSECT SCIENCE 2018; 18:7. [PMCID: PMC5786230 DOI: 10.1093/jisesa/iex111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Indexed: 06/11/2023]
Abstract
Trehalose is the major blood sugar in insects. Physiological significance of this compound has been extensively reported. Trehalose-6-phosphate synthase (TPS) is an important enzyme in the trehalose biosynthesis pathway. Full-length cDNAs of TPS (Of tps) and its alternative splicing isoform (Of tps_isoformI) were cloned from the Asian corn borer (ACB), Ostrinia furnacalis (Guenée; Lepidoptera: Crambidae) larvae. The Of tps and Of tps_isoformI transcripts were 2913 and 1689 bp long, contained 2529 and 1293 bp open reading frames encoding proteins of 842 and 430 amino acids with a molecular mass of 94.4 and 48.6 kDa, respectively. Transcriptional profiling and response to thermal stress of Of tps gene were determined by quantitative real-time PCR showing that the Of tps was predominantly expressed in the larval fat body, significantly enhanced during molting and transformation; and thermal stress also induced Of tps expression. Gene structure analysis is indicating that one TPS domain and one trehalose-6-phosphate phosphatase (TPP) domain were located at the N- and C-termini of Of TPS, respectively, while only the TPS domain was detected in OfTPS_isoformI. Three-dimensional modeling and heterologous expression were developed to predict the putative functions of OfTPS and Of TPS_isoformI. We infer that the expression of Of tps gene is thermally induced and might be crucial for larvae survival.
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Affiliation(s)
- Tingting Jin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, China
- State Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, China
| | - Yulin Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, China
| | - Kanglai He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, China
| | - Feng Ge
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, China
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30
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Glycerol-3-phosphate phosphatase/PGP: Role in intermediary metabolism and target for cardiometabolic diseases. Biochimie 2017; 143:18-28. [PMID: 28826615 DOI: 10.1016/j.biochi.2017.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/02/2017] [Indexed: 11/22/2022]
Abstract
Metabolic diseases, including obesity, type 2 diabetes, and metabolic syndrome arise because of disturbances in glucose and fat metabolism, which impact associated physiological events such as insulin secretion and action, fat storage and oxidation. Even though, decades of research has contributed to our current understanding of the components involved in glucose and fat metabolism and their regulation, that led to the development of many therapeutics, there are still many unanswered questions. Glycerol-3-phosphate (Gro3P), which is formed during glycolysis, is at the intersection of glucose and fat metabolism, and the availability of this metabolite can regulate energy and intermediary metabolism in mammalian cells. During the course of evolution, mammalian cells are assumed to have lost the capacity to directly hydrolyze Gro3P to glycerol, until the recent discovery from our laboratory showing that a previously known mammalian enzyme, phosphoglycolate phosphatase (PGP), can function as a Gro3P phosphatase (G3PP) and regulate this metabolite levels. Emerging evidence indicates that G3PP/PGP is an evolutionarily conserved "multi-tasking" enzyme that belongs to the superfamily of haloacid dehalogenase-like phosphatase enzymes, and is capable of hydrolyzing Gro3P, an abundant physiologically relevant substrate, as well as other metabolites including 2-phosphoglycolate, 4-phosphoerythronate and 2-phospholactate, which are present in much smaller amounts in cells, under normal conditions. G3PP, by regulating Gro3P levels, plays a critical role in intermediary metabolism, including glycolysis, glucose oxidation, cellular redox and ATP production, gluconeogenesis, esterification of fatty acids towards glycerolipid synthesis and fatty acid oxidation. Because of G3PP's ability to regulate energy and intermediary metabolism as well as physiological functions such as insulin secretion, hepatic glucose production, and fat synthesis, storage and oxidation, the pathophysiological role of this enzyme in metabolic diseases needs to be precisely defined. In this review, we summarize the present knowledge on the structure, function and regulation of G3PP/PGP, and we discuss its potential therapeutic role for cardiometabolic diseases.
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31
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Analysis of a dual domain phosphoglycosyl transferase reveals a ping-pong mechanism with a covalent enzyme intermediate. Proc Natl Acad Sci U S A 2017. [PMID: 28630348 DOI: 10.1073/pnas.1703397114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Phosphoglycosyl transferases (PGTs) are integral membrane proteins with diverse architectures that catalyze the formation of polyprenol diphosphate-linked glycans via phosphosugar transfer from a nucleotide diphosphate-sugar to a polyprenol phosphate. There are two PGT superfamilies that differ significantly in overall structure and topology. The polytopic PGT superfamily, represented by MraY and WecA, has been the subject of many studies because of its roles in peptidoglycan and O-antigen biosynthesis. In contrast, less is known about a second, extensive superfamily of PGTs that reveals a core structure with dual domain architecture featuring a C-terminal soluble globular domain and a predicted N-terminal membrane-associated domain. Representative members of this superfamily are the Campylobacter PglCs, which initiate N-linked glycoprotein biosynthesis and are implicated in virulence and pathogenicity. Despite the prevalence of dual domain PGTs, their mechanism of action is unknown. Here, we present the mechanistic analysis of PglC, a prototypic dual domain PGT from Campylobacter concisus Using a luminescence-based assay, together with substrate labeling and kinetics-based approaches, complementary experiments were carried out that support a ping-pong mechanism involving a covalent phosphosugar intermediate for PglC. Significantly, mass spectrometry-based approaches identified Asp93, which is part of a highly conserved AspGlu dyad found in all dual domain PGTs, as the active-site nucleophile of the enzyme involved in the formation of the covalent adduct. The existence of a covalent phosphosugar intermediate provides strong support for a ping-pong mechanism of PglC, differing fundamentally from the ternary complex mechanisms of representative polytopic PGTs.
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Morales-Sánchez D, Kim Y, Terng EL, Peterson L, Cerutti H. A multidomain enzyme, with glycerol-3-phosphate dehydrogenase and phosphatase activities, is involved in a chloroplastic pathway for glycerol synthesis in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1079-1092. [PMID: 28273364 DOI: 10.1111/tpj.13530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 02/06/2017] [Accepted: 02/28/2017] [Indexed: 05/20/2023]
Abstract
Understanding the unique features of algal metabolism may be necessary to realize the full potential of algae as feedstock for the production of biofuels and biomaterials. Under nitrogen deprivation, the green alga C. reinhardtii showed substantial triacylglycerol (TAG) accumulation and up-regulation of a gene, GPD2, encoding a multidomain enzyme with a putative phosphoserine phosphatase (PSP) motif fused to glycerol-3-phosphate dehydrogenase (GPD) domains. Canonical GPD enzymes catalyze the synthesis of glycerol-3-phosphate (G3P) by reduction of dihydroxyacetone phosphate (DHAP). G3P forms the backbone of TAGs and membrane glycerolipids and it can be dephosphorylated to yield glycerol, an osmotic stabilizer and compatible solute under hypertonic stress. Recombinant Chlamydomonas GPD2 showed both reductase and phosphatase activities in vitro and it can work as a bifunctional enzyme capable of synthesizing glycerol directly from DHAP. In addition, GPD2 and a gene encoding glycerol kinase were up-regulated in Chlamydomonas cells exposed to high salinity. RNA-mediated silencing of GPD2 revealed that the multidomain enzyme was required for TAG accumulation under nitrogen deprivation and for glycerol synthesis under high salinity. Moreover, a GPD2-mCherry fusion protein was found to localize to the chloroplast, supporting the existence of a GPD2-dependent plastid pathway for the rapid synthesis of glycerol in response to hyperosmotic stress. We hypothesize that the reductase and phosphatase activities of PSP-GPD multidomain enzymes may be modulated by post-translational modifications/mechanisms, allowing them to synthesize primarily G3P or glycerol depending on environmental conditions and/or metabolic demands in algal species of the core Chlorophytes.
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Affiliation(s)
- Daniela Morales-Sánchez
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Yeongho Kim
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Ee Leng Terng
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Laura Peterson
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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Zhou Y, Hölzl G, Vom Dorp K, Peisker H, Melzer M, Frentzen M, Dörmann P. Identification and characterization of a plastidial phosphatidylglycerophosphate phosphatase in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:221-234. [PMID: 27614107 DOI: 10.1111/tpj.13378] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/30/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
Phosphatidylglycerol (PG) is the only phospholipid in the thylakoid membranes of chloroplasts of plants, and it is also found in extraplastidial membranes including mitochondria and the endoplasmic reticulum. Previous studies showed that lack of PG in the pgp1-2 mutant of Arabidopsis deficient in phosphatidylglycerophosphate (PGP) synthase strongly affects thylakoid biogenesis and photosynthetic activity. In the present study, the gene encoding the enzyme for the second step of PG synthesis, PGP phosphatase, was isolated based on sequence similarity to the yeast GEP4 and Chlamydomonas PGPP1 genes. The Arabidopsis AtPGPP1 protein localizes to chloroplasts and harbors PGP phosphatase activity with alkaline pH optimum and divalent cation requirement. Arabidopsis pgpp1-1 mutant plants contain reduced amounts of chlorophyll, but photosynthetic quantum yield remains unchanged. The absolute content of plastidial PG (34:4; total number of acyl carbons:number of double bonds) is reduced by about 1/3, demonstrating that AtPGPP1 is involved in the synthesis of plastidial PG. PGP 34:3, PGP 34:2 and PGP 34:1 lacking 16:1 accumulate in pgpp1-1, indicating that the desaturation of 16:0 to 16:1 by the FAD4 desaturase in the chloroplasts only occurs after PGP dephosphorylation.
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Affiliation(s)
- Yonghong Zhou
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
| | - Georg Hölzl
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
| | - Katharina Vom Dorp
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
| | - Helga Peisker
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
| | - Michael Melzer
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Margrit Frentzen
- Botany, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
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Albi T, Ruiz MT, de los Reyes P, Valverde F, Romero JM. Characterization of the Sucrose Phosphate Phosphatase (SPP) Isoforms from Arabidopsis thaliana and Role of the S6PPc Domain in Dimerization. PLoS One 2016; 11:e0166308. [PMID: 27855180 PMCID: PMC5113954 DOI: 10.1371/journal.pone.0166308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/26/2016] [Indexed: 12/16/2022] Open
Abstract
Sucrose-phosphate phosphatase (SPP) catalyses the final step in the sucrose biosynthesis pathway. Arabidopsis thaliana genome codifies four SPP isoforms. In this study, the four Arabidopsis thaliana genes coding for SPP isoforms have been cloned, expressed in Escherichia coli and the kinetic and regulatory properties of the purified enzymes analysed. SPP2 is the isoform showing the highest activity, with SPP3b and SPP3a showing lower activity levels. No activity was detected for SPP1. We propose that this lack of activity is probably due to the absence of an essential amino acid participating in catalysis and/or in the binding of the substrate, sucrose-6-phosphate (Suc6P). The expression patterns of Arabidopsis SPP genes indicate that SPP2 and SPP3b are the main isoforms expressed in different tissues and organs, although the non-catalytic SPP1 is the main isoform expressed in roots. Thus, SPP1 could have acquired new unknown functions. We also show that the three catalytically active SPPs from Arabidopsis are dimers. By generating a chimeric SPP composed of the monomeric cyanobacterial SPP fused to the higher plant non-catalytic S6PPc domain (from SPP2), we show that the S6PPc domain is responsible for SPP dimerization. This is the first experimental study on the functionality and gene expression pattern of all the SPPs from a single plant species.
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Affiliation(s)
- Tomás Albi
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - M. Teresa Ruiz
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Pedro de los Reyes
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Federico Valverde
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - José M. Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Seville, Spain
- * E-mail:
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35
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Gogoi P, Chandravanshi M, Mandal SK, Srivastava A, Kanaujia SP. Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies. J Biomol Struct Dyn 2015; 34:1470-85. [PMID: 26248730 DOI: 10.1080/07391102.2015.1080629] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca(2+), Mg(2+), Zn(2+), Fe(2+), Cu(2+), Ba(2+), and Sr(2+), respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe(2+) and Cu(2+), respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature.
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Affiliation(s)
- Prerana Gogoi
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Monika Chandravanshi
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Suraj Kumar Mandal
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Ambuj Srivastava
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Shankar Prasad Kanaujia
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
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Haimovich-Dayan M, Lieman-Hurwitz J, Orf I, Hagemann M, Kaplan A. Does 2-phosphoglycolate serve as an internal signal molecule of inorganic carbon deprivation in the cyanobacterium Synechocystis sp. PCC 6803? Environ Microbiol 2015; 17:1794-804. [PMID: 25297829 DOI: 10.1111/1462-2920.12638] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
Cyanobacteria possess CO2 -concentrating mechanisms (CCM) that functionally compensate for the poor affinity of their ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to CO2 . It was proposed that 2-phosphoglycolate (2PG), produced by the oxygenase activity of Rubisco and metabolized via photorespiratory routes, serves as a signal molecule for the induction of CCM-related genes under limiting CO2 level (LC) conditions. However, in vivo evidence is still missing. Since 2PG does not permeate the cells, we manipulated its internal concentration. Four putative phosphoglycolate phosphatases (PGPases) encoding genes (slr0458, sll1349, slr0586 and slr1762) were identified in the cyanobacterium Synechocystis PCC 6803. Expression of slr0458 in Escherichia coli led to a significant rise in PGPase activity. A Synechocystis mutant overexpressing (OE) slr0458 was constructed. Compared with the wild type (WT), the mutant grew slower under limiting CO2 concentration and the intracellular 2PG level was considerably smaller than in the wild type, the transcript abundance of LC-induced genes including cmpA, sbtA and ndhF3 was reduced, and the OE cells acclimated slower to LC - indicated by the delayed rise in the apparent photosynthetic affinity to inorganic carbon. Data obtained here implicated 2PG in the acclimation of this cyanobacterium to LC but also indicated that other, yet to be identified components, are involved.
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Affiliation(s)
- Maya Haimovich-Dayan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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37
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London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry 2015; 54:528-37. [PMID: 25513739 PMCID: PMC4303301 DOI: 10.1021/bi501140k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Enzyme function prediction remains
an important open problem. Though
structure-based modeling, such as metabolite docking, can identify
substrates of some enzymes, it is ill-suited to reactions that progress
through a covalent intermediate. Here we investigated the ability
of covalent docking to identify substrates that pass through such
a covalent intermediate, focusing particularly on the haloalkanoate
dehalogenase superfamily. In retrospective assessments, covalent docking
recapitulated substrate binding modes of known cocrystal structures
and identified experimental substrates from a set of putative phosphorylated
metabolites. In comparison, noncovalent docking of high-energy intermediates
yielded nonproductive poses. In prospective predictions against seven
enzymes, a substrate was identified for five. For one of those cases,
a covalent docking prediction, confirmed by empirical screening, and
combined with genomic context analysis, suggested the identity of
the enzyme that catalyzes the orphan phosphatase reaction in the riboflavin
biosynthetic pathway of Bacteroides.
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Affiliation(s)
- Nir London
- Department of Pharmaceutical Chemistry, and §Department of Bioengineering and Therapeutic Sciences, University of California San Francisco , San Francisco, California 94158, United States
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38
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Kilaparty SP, Singh A, Baltosser WH, Ali N. Computational analysis reveals a successive adaptation of multiple inositol polyphosphate phosphatase 1 in higher organisms through evolution. Evol Bioinform Online 2014; 10:239-50. [PMID: 25574123 PMCID: PMC4275298 DOI: 10.4137/ebo.s18948] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/29/2014] [Accepted: 10/05/2014] [Indexed: 11/05/2022] Open
Abstract
Multiple inositol polyphosphate phosphatase 1 (Minpp1) in higher organisms dephosphorylates InsP6, the most abundant inositol phosphate. It also dephosphorylates less phosphorylated InsP5 and InsP4 and more phosphorylated InsP7 or InsP8. Minpp1 is classified as a member of the histidine acid phosphatase super family of proteins with functional resemblance to phytases found in lower organisms. This study took a bioinformatics approach to explore the extent of evolutionary diversification in Minpp1 structure and function in order to understand its physiological relevance in higher organisms. The human Minpp1 amino acid (AA) sequence was BLAST searched against available national protein databases. Phylogenetic analysis revealed that Minpp1 was widely distributed from lower to higher organisms. Further, we have identified that there exist four isoforms of Minpp1. Multiple computational tools were used to identify key functional motifs and their conservation among various species. Analyses showed that certain motifs predominant in higher organisms were absent in lower organisms. Variation in AA sequences within motifs was also analyzed. We found that there is diversification of key motifs and thus their functions present in Minpp1 from lower organisms to higher organisms. Another interesting result of this analysis was the presence of a glucose-1-phosphate interaction site in Minpp1; the functional significance of which has yet to be determined experimentally. The overall findings of our study point to an evolutionary adaptability of Minpp1 functions from lower to higher life forms.
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Affiliation(s)
- Surya P Kilaparty
- Department of Biology, University of Arkansas at Little Rock, Arkansas, USA
| | - Awantika Singh
- UAMS/UALR Joint Bioinformatics Program, University of Arkansas at Little Rock, Arkansas, USA
| | | | - Nawab Ali
- Department of Biology, University of Arkansas at Little Rock, Arkansas, USA
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Phosphoryl transfer from α-d-glucose 1-phosphate catalyzed by Escherichia coli sugar-phosphate phosphatases of two protein superfamily types. Appl Environ Microbiol 2014; 81:1559-72. [PMID: 25527541 DOI: 10.1128/aem.03314-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Cori ester α-d-glucose 1-phosphate (αGlc 1-P) is a high-energy intermediate of cellular carbohydrate metabolism. Its glycosidic phosphomonoester moiety primes αGlc 1-P for flexible exploitation in glucosyl and phosphoryl transfer reactions. Two structurally and mechanistically distinct sugar-phosphate phosphatases from Escherichia coli were characterized in this study for utilization of αGlc 1-P as a phosphoryl donor substrate. The agp gene encodes a periplasmic αGlc 1-P phosphatase (Agp) belonging to the histidine acid phosphatase family. Had13 is from the haloacid dehydrogenase-like phosphatase family. Cytoplasmic expression of Agp (in E. coli Origami B) gave a functional enzyme preparation (kcat for phosphoryl transfer from αGlc 1-P to water, 40 s(-1)) that was shown by mass spectrometry to exhibit no free cysteines and the native intramolecular disulfide bond between Cys(189) and Cys(195). Enzymatic phosphoryl transfer from αGlc 1-P to water in H2 (18)O solvent proceeded with complete (18)O label incorporation into the phosphate released, consistent with catalytic reaction through O-1-P, but not C-1-O, bond cleavage. Hydrolase activity of both enzymes was not restricted to a glycosidic phosphomonoester substrate, and d-glucose 6-phosphate was converted with a kcat similar to that of αGlc 1-P. By examining phosphoryl transfer from αGlc 1-P to an acceptor substrate other than water (d-fructose or d-glucose), we discovered that Agp exhibited pronounced synthetic activity, unlike Had13, which utilized αGlc 1-P mainly for phosphoryl transfer to water. By applying d-fructose in 10-fold molar excess over αGlc 1-P (20 mM), enzymatic conversion furnished d-fructose 1-phosphate as the main product in a 55% overall yield. Agp is a promising biocatalyst for use in transphosphorylation from αGlc 1-P.
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40
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Caparrós-Martín JA, McCarthy-Suárez I, Culiáñez-Macià FA. The kinetic analysis of the substrate specificity of motif 5 in a HAD hydrolase-type phosphosugar phosphatase of Arabidopsis thaliana. PLANTA 2014; 240:479-487. [PMID: 24915748 DOI: 10.1007/s00425-014-2102-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/16/2014] [Indexed: 06/03/2023]
Abstract
The Arabidopsis thaliana gene AtSgpp (locus tag At2g38740), encodes a protein whose sequence motifs and expected structure reveal that it belongs to the HAD hydrolases subfamily I, with the C1-type cap domain (Caparrós-Martín et al. in Planta 237:943-954, 2013). In the presence of Mg(2+) ions, the enzyme has a phosphatase activity over a wide range of phosphosugar substrates. AtSgpp promiscuity is preferentially detectable on D-ribose-5-phosphate, 2-deoxy-D-ribose-5-phosphate, 2-deoxy-D-glucose-6-phosphate, D-mannose-6-phosphate, D-fructose-1-phosphate, D-glucose-6-phosphate, DL-glycerol-3-phosphate, and D-fructose-6-phosphate. Site-directed mutagenesis analysis of the putative signature sequence motif-5 (IAGKH), which defines its specific chemistry, brings to light the active-site residues Ala-69 and His-72. Mutation A69M, changes the pH dependence of AtSgpp catalysis, and mutant protein AtSgpp-H72K was inactive in phosphomonoester dephosphorylation. It was also observed that substitutions I68M and K71R slightly affect the substrate specificity, while the replacement of the entire motif for that of homologous DL-glycerol-3-phosphatase AtGpp (MMGRK) does not switch AtSgpp activity to the specific targeting for DL-glycerol-3-phosphate.
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Affiliation(s)
- José A Caparrós-Martín
- Instituto de Biología Molecular y Celular de Plantas "Eduardo Primo Yúfera" (UPV-CSIC), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación (CPI), C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
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41
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Sand M, Rodrigues M, González JM, de Crécy-Lagard V, Santos H, Müller V, Averhoff B. Mannitol-1-phosphate dehydrogenases/phosphatases: a family of novel bifunctional enzymes for bacterial adaptation to osmotic stress. Environ Microbiol 2014; 17:711-9. [DOI: 10.1111/1462-2920.12503] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 04/30/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Miriam Sand
- Molecular Microbiology & Bioenergetics; Institute of Molecular Biosciences; Johann Wolfgang Goethe University Frankfurt am Main; Frankfurt Germany
| | - Marta Rodrigues
- Cell Physiology and NMR Lab; Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - José M. González
- Department of Microbiology; University of La Laguna; La Laguna Tenerife Spain
| | | | - Helena Santos
- Cell Physiology and NMR Lab; Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Volker Müller
- Molecular Microbiology & Bioenergetics; Institute of Molecular Biosciences; Johann Wolfgang Goethe University Frankfurt am Main; Frankfurt Germany
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics; Institute of Molecular Biosciences; Johann Wolfgang Goethe University Frankfurt am Main; Frankfurt Germany
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Monecke T, Buschmann J, Neumann P, Wahle E, Ficner R. Crystal structures of the novel cytosolic 5'-nucleotidase IIIB explain its preference for m7GMP. PLoS One 2014; 9:e90915. [PMID: 24603684 PMCID: PMC3946280 DOI: 10.1371/journal.pone.0090915] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/04/2014] [Indexed: 12/13/2022] Open
Abstract
5′-nucleotidases catalyze the hydrolytic dephosphorylation of nucleoside monophosphates. As catabolic enzymes they contribute significantly to the regulation of cellular nucleotide levels; misregulation of nucleotide metabolism and nucleotidase deficiencies are associated with a number of diseases. The seven human 5′-nucleotidases differ with respect to substrate specificity and cellular localization. Recently, the novel cytosolic 5′-nucleotidase III-like protein, or cN-IIIB, has been characterized in human and Drosophila. cN-IIIB exhibits a strong substrate preference for the modified nucleotide 7-methylguanosine monophosphate but the structural reason for this preference was unknown. Here, we present crystal structures of cN-IIIB from Drosophila melanogaster bound to the reaction products 7-methylguanosine or cytidine. The structural data reveal that the cytosine- and 7-methylguanine moieties of the products are stacked between two aromatic residues in a coplanar but off-centered position. 7-methylguanosine is specifically bound through π-π interactions and distinguished from unmodified guanosine by additional cation-π coulomb interactions between the aromatic side chains and the positively charged 7-methylguanine. Notably, the base is further stabilized by T-shaped edge-to-face stacking of an additional tryptophan packing perpendicularly against the purine ring and forming, together with the other aromates, an aromatic slot. The structural data in combination with site-directed mutagenesis experiments reveal the molecular basis for the broad substrate specificity of cN-IIIB but also explain the substrate preference for 7-methylguanosine monophosphate. Analyzing the substrate specificities of cN-IIIB and the main pyrimidine 5′-nucleotidase cN-IIIA by mutagenesis studies, we show that cN-IIIA dephosphorylates the purine m7GMP as well, hence redefining its substrate spectrum. Docking calculations with cN-IIIA and m7GMP as well as biochemical data reveal that Asn69 does not generally exclude the turnover of purine substrates thus correcting previous suggestions.
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Affiliation(s)
- Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail:
| | - Juliane Buschmann
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Piotr Neumann
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Elmar Wahle
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
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43
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Deng Y, Wang X, Guo H, Duan D. A trehalose-6-phosphate synthase gene from Saccharina japonica (Laminariales, Phaeophyceae). Mol Biol Rep 2014; 41:529-36. [PMID: 24293128 DOI: 10.1007/s11033-013-2888-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 11/25/2013] [Indexed: 10/26/2022]
Abstract
The full-length cDNA sequence of a trehalose-6-phosphate synthase gene from Saccharina japonica (designated as SjaTPS) (Accession: KC578568) was isolated based on homologous cloning and RACE-PCR. It was 4,127 bp, with 320 bp 5'-UTR, 21 bp 3'-UTR, and open reading frame (ORF) of 3,786 bp. The deduced 1,261 amino acids characterized with predicted molecular weight of 137.84 kDa and theoretical isoelectric point of 7.12. The SjaTPS had one N-terminal CBM20 (family 20 carbohydrate-binding module) domain, one TPS domain (trehalose-6-phosphate synthase) in the middle region and a single TPP (trehalose-6-phosphate phosphatase) domain near the C-terminus. Structural analysis suggested that the SjaTPS putatively functioned as trehalose-6-phosphate synthase, and might be related to laminaran metabolism in S. japonica. Homology analysis indicated that the SjaTPS shared 49-70 % similarities with the 13 known TPS sequences of other algae; only 55 % amino acid similarities were detected between SjaTPS and the previously reported TPS sequence of S. japonica (Accession: DQ666325). Phylogenetic analysis revealed close affinity between SjaTPS and TPS of brown alga Ectocarpus siliculosus (Accession: CBJ29609). Transcriptional analysis showed that desiccation greatly enhanced SjaTPS expression and the maximum appeared at 3 h, which was about 300-fold compared to that of the start, implied that SjaTPS was involved with drought adaption in kelp. In vitro expression of SjaTPS showed that one distinct band existed at ~115 kDa, and western blot detection proved that it was positive to the anti-His antibody with high specificity. Our results increased the knowledge of trehalose-6-phosphate synthase properties in S. japonica and also important for better understanding the role trehalose plays in kelp abiotic tolerance for adaption to the sublittoral habitats.
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Affiliation(s)
- Yunyan Deng
- Chinese Academy of Sciences, Institute of Oceanology, Qingdao, 266071, China,
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Zhang D, Song H, Cheng H, Hao D, Wang H, Kan G, Jin H, Yu D. The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. PLoS Genet 2014; 10:e1004061. [PMID: 24391523 PMCID: PMC3879153 DOI: 10.1371/journal.pgen.1004061] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 11/11/2013] [Indexed: 01/12/2023] Open
Abstract
Phosphorus (P) is essential for all living cells and organisms, and low-P stress is a major factor constraining plant growth and yield worldwide. In plants, P efficiency is a complex quantitative trait involving multiple genes, and the mechanisms underlying P efficiency are largely unknown. Combining linkage analysis, genome-wide and candidate-gene association analyses, and plant transformation, we identified a soybean gene related to P efficiency, determined its favorable haplotypes and developed valuable functional markers. First, six major genomic regions associated with P efficiency were detected by performing genome-wide associations (GWAs) in various environments. A highly significant region located on chromosome 8, qPE8, was identified by both GWAs and linkage mapping and explained 41% of the phenotypic variation. Then, a regional mapping study was performed with 40 surrounding markers in 192 diverse soybean accessions. A strongly associated haplotype (P = 10(-7)) consisting of the markers Sat_233 and BARC-039899-07603 was identified, and qPE8 was located in a region of approximately 250 kb, which contained a candidate gene GmACP1 that encoded an acid phosphatase. GmACP1 overexpression in soybean hairy roots increased P efficiency by 11-20% relative to the control. A candidate-gene association analysis indicated that six natural GmACP1 polymorphisms explained 33% of the phenotypic variation. The favorable alleles and haplotypes of GmACP1 associated with increased transcript expression correlated with higher enzyme activity. The discovery of the optimal haplotype of GmACP1 will now enable the accurate selection of soybeans with higher P efficiencies and improve our understanding of the molecular mechanisms underlying P efficiency in plants.
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Affiliation(s)
- Dan Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Department of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haina Song
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Derong Hao
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Hui Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Hangxia Jin
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- National Center of Plant Gene Research (Shanghai), Shanghai, China
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Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
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Caparrós-Martín JA, McCarthy-Suárez I, Culiáñez-Macià FA. HAD hydrolase function unveiled by substrate screening: enzymatic characterization of Arabidopsis thaliana subclass I phosphosugar phosphatase AtSgpp. PLANTA 2013; 237:943-54. [PMID: 23179445 PMCID: PMC3607736 DOI: 10.1007/s00425-012-1809-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 11/02/2012] [Indexed: 05/18/2023]
Abstract
This work presents the isolation and the biochemical characterization of the Arabidopsis thaliana gene AtSgpp. This gene shows homology with the Arabidopsis low molecular weight phosphatases AtGpp1 and AtGpp2 and the yeast counterpart GPP1 and GPP2, which have a high specificity for DL-glycerol-3-phosphate. In addition, it exhibits homology with DOG1 and DOG2 that dephosphorylate 2-deoxy-D-glucose-6-phosphate. Using a comparative genomic approach, we identified the AtSgpp gene as a conceptual translated haloacid dehalogenase-like hydrolase HAD protein. AtSgpp (locus tag At2g38740), encodes a protein with a predicted Mw of 26.7 kDa and a pI of 4.6. Its sequence motifs and expected structure revealed that AtSgpp belongs to the HAD hydrolases subfamily I, with the C1-type cap domain. In the presence of Mg(2+) ions, the enzyme has a phosphatase activity over a wide range of phosphosugars substrates (pH optima at 7.0 and K m in the range of 3.6-7.7 mM). AtSgpp promiscuity is preferentially detectable on D-ribose-5-phosphate, 2-deoxy-D-ribose-5-phosphate, 2-deoxy-D-glucose-6-phosphate, D-mannose-6-phosphate, D-fructose-1-phosphate, D-glucose-6-phosphate, DL-glycerol-3-phosphate, and D-fructose-6-phosphate, as substrates. AtSgpp is ubiquitously expressed throughout development in most plant organs, mainly in sepal and guard cell. Interestingly, expression is affected by abiotic and biotic stresses, being the greatest under Pi starvation and cyclopentenone oxylipins induction. Based on both, substrate lax specificity and gene expression, the physiological function of AtSgpp in housekeeping detoxification, modulation of sugar-phosphate balance and Pi homeostasis, is provisionally assigned.
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Affiliation(s)
- José A. Caparrós-Martín
- Instituto de Biología Molecular y Celular de Plantas ‘‘Eduardo Primo Yúfera’’ (UPV-CSIC), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación (CPI), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Iva McCarthy-Suárez
- Instituto de Biología Molecular y Celular de Plantas ‘‘Eduardo Primo Yúfera’’ (UPV-CSIC), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación (CPI), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Francisco A. Culiáñez-Macià
- Instituto de Biología Molecular y Celular de Plantas ‘‘Eduardo Primo Yúfera’’ (UPV-CSIC), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación (CPI), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
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Teh PG, Chen MJ, Engel JL, Worby CA, Manning G, Dixon JE, Zhang J. Identification of a mammalian-type phosphatidylglycerophosphate phosphatase in the Eubacterium Rhodopirellula baltica. J Biol Chem 2013; 288:5176-85. [PMID: 23293031 PMCID: PMC3576122 DOI: 10.1074/jbc.m112.413617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cardiolipin is a glycerophospholipid found predominantly in the mitochondrial membranes of eukaryotes and in bacterial membranes. Cardiolipin interacts with protein complexes and plays pivotal roles in cellular energy metabolism, membrane dynamics, and stress responses. We recently identified the mitochondrial phosphatase, PTPMT1, as the enzyme that converts phosphatidylglycerolphosphate (PGP) to phosphatidylglycerol, a critical step in the de novo biosynthesis of cardiolipin. Upon examination of PTPMT1 evolutionary distribution, we found a PTPMT1-like phosphatase in the bacterium Rhodopirellula baltica. The purified recombinant enzyme dephosphorylated PGP in vitro. Moreover, its expression restored cardiolipin deficiency and reversed growth impairment in a Saccharomyces cerevisiae mutant lacking the yeast PGP phosphatase, suggesting that it is a bona fide PTPMT1 ortholog. When ectopically expressed, this bacterial PGP phosphatase was localized in the mitochondria of yeast and mammalian cells. Together, our results demonstrate the conservation of function between bacterial and mammalian PTPMT1 orthologs.
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Affiliation(s)
- Phildrich G Teh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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Zheng J, Yates SP, Jia Z. Structural and mechanistic insights into the bifunctional enzyme isocitrate dehydrogenase kinase/phosphatase AceK. Philos Trans R Soc Lond B Biol Sci 2012; 367:2656-68. [PMID: 22889914 DOI: 10.1098/rstb.2011.0426] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The switch between the Krebs cycle and the glyoxylate bypass is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK). AceK, a bifunctional enzyme, phosphorylates and dephosphorylates isocitrate dehydrogenase (IDH) with its unique active site that harbours both the kinase and ATP/ADP-dependent phosphatase activities. AceK was the first example of prokaryotic phosphorylation identified, and the recent characterization of the structures of AceK and its complex with its protein substrate, IDH, now offers a new understanding of both previous and future endeavours. AceK is structurally similar to the eukaryotic protein kinase superfamily, sharing many of the familiar catalytic and regulatory motifs, demonstrating a close evolutionary relationship. Although the active site is shared by both the kinase and phosphatase functions, the catalytic residues needed for phosphatase function are readily seen when compared with the DXDX(T/V) family of phosphatases, despite the fact that the phosphatase function of AceK is strictly ATP/ADP-dependent. Structural analysis has also allowed a detailed look at regulation and its stringent requirements for interacting with IDH.
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Affiliation(s)
- Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit. Nat Struct Mol Biol 2012; 19:1316-23. [PMID: 23104056 PMCID: PMC3515705 DOI: 10.1038/nsmb.2403] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/10/2012] [Indexed: 11/09/2022]
Abstract
Ribosome synthesis involves dynamic association of ribosome-biogenesis factors with evolving preribosomal particles. Rio2 is an atypical protein kinase required for pre-40S subunit maturation. We report the crystal structure of eukaryotic Rio2-ATP-Mg(2+) complex. The active site contains ADP-Mg(2+) and a phosphoaspartate intermediate typically found in Na(+), K(+) and Ca(2+) ATPases but not protein kinases. Consistent with this finding, ctRio2 exhibits a robust ATPase activity in vitro. In vivo, Rio2 docks on the ribosome, with its active site occluded and its flexible loop positioned to interact with the pre-40S subunit. Moreover, Rio2 catalytic activity is required for its dissociation from the ribosome, a necessary step in pre-40S maturation. We propose that phosphoryl transfer from ATP to Asp257 in Rio2's active site and subsequent hydrolysis of the aspartylphosphate could be a trigger to power late cytoplasmic 40S subunit biogenesis.
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Yang L, Liao RZ, Ding WJ, Liu K, Yu JG, Liu RZ. Why calcium inhibits magnesium-dependent enzyme phosphoserine phosphatase? A theoretical study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1275-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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