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Li Q, Wang Z, Zhu M, Zhao W, Yu S. Metabolism of Inulin via Difructose Anhydride I Pathway in Microbacterium flavum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9647-9655. [PMID: 38629750 DOI: 10.1021/acs.jafc.4c00729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Difructose anhydride I (DFA-I) can be produced from inulin, with DFA-I-forming inulin fructotransferase (IFTase-I). However, the metabolism of inulin through DFA-I remains unclear. To clarify this pathway, several genes of enzymes related to this pathway in the genome of Microbacterium flavum DSM 18909 were synthesized, and the corresponding enzymes were encoded, purified, and investigated in vitro. After inulin is decomposed to DFA-I by IFTase-I, DFA-I is hydrolyzed to inulobiose by DFA-I hydrolase. Inulobiose is then hydrolyzed by β-fructofuranosidase to form fructose. Finally, fructose enters glycolysis through fructokinase. A β-fructofuranosidase (MfFFase1) clears the byproducts (sucrose and fructo-oligosaccharides), which might be partially hydrolyzed by fructan β-(2,1)-fructosidase/1-exohydrolase and another fructofuranosidase (MfFFase2). Exploring the DFA-I pathway of inulin and well-studied enzymes in vitro extends our basic scientific knowledge of the energy-providing way of inulin, thereby paving the way for further investigations in vivo and offering a reference for further nutritional investigation of inulin and DFA-I in the future.
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Affiliation(s)
- Qiting Li
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Zhenlong Wang
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Mengyan Zhu
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Wei Zhao
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Shuhuai Yu
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
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do Prado PFV, Ahrens FM, Liebers M, Ditz N, Braun HP, Pfannschmidt T, Hillen HS. Structure of the multi-subunit chloroplast RNA polymerase. Mol Cell 2024; 84:910-925.e5. [PMID: 38428434 DOI: 10.1016/j.molcel.2024.02.003] [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: 09/25/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression.
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Affiliation(s)
- Paula F V do Prado
- University Medical Center Göttingen, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Research Group Structure and Function of Molecular Machines, Am Fassberg 11, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Frederik M Ahrens
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Monique Liebers
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Noah Ditz
- Institute of Plant Genetics, Plant Molecular Biology and Plant Proteomics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Plant Molecular Biology and Plant Proteomics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Thomas Pfannschmidt
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Hauke S Hillen
- University Medical Center Göttingen, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Research Group Structure and Function of Molecular Machines, Am Fassberg 11, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Research Group Structure and Function of Molecular Machines, University of Göttingen, 37077 Göttingen, Germany.
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Gao B, Ji R, Li Z, Su X, Li H, Sun Y, Ji C, Gan J, Li J. Structural analysis and functional study of phosphofructokinase B (PfkB) from Mycobacterium marinum. Biochem Biophys Res Commun 2021; 579:129-135. [PMID: 34597996 DOI: 10.1016/j.bbrc.2021.09.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 11/27/2022]
Abstract
Phosphofructokinase B (PfkB) belongs to the ribokinase family, which uses the phosphorylated sugar as substrate, and catalyzes fructose-6-phosphate into fructose-1,6-diphosphate. However, the structural basis of Mycobacterium marinum PfkB is not clear. Here, we found that the PfkB protein was monomeric in solution, which was different from most enzymes in this family. The crystal structure of PfkB protein from M. marinum was solved at a resolution of 2.21 Å. The PfkB structure consists of two domains, a major three-layered α/β/α sandwich-like domain characteristic of the ribokinase-like superfamily, and a second domain composed of four-stranded β sheets. Structural comparison analysis suggested that residues G236, A237, G238, and D239 could be critical for ATP catalysis and substrate binding of PfkB. Our current work provides new insights into understanding the mechanism of the glycolysis in M. marinum.
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Affiliation(s)
- Baocai Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Xiaoqin Su
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Hongyong Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Yicheng Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, And Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.
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Gatreddi S, Pillalamarri V, Vasudevan D, Addlagatta A, Qureshi IA. Unraveling structural insights of ribokinase from Leishmania donovani. Int J Biol Macromol 2019; 136:253-265. [PMID: 31170491 DOI: 10.1016/j.ijbiomac.2019.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/29/2019] [Accepted: 06/01/2019] [Indexed: 11/16/2022]
Abstract
Ribokinase (RK) is an ATP dependent sugar kinase that enables the entry of ribose in the metabolism. Leishmania accumulates ribose into the cytosol through hydrolysis of nucleosides and by transport from the extracellular environment. Activation by RK is critical to mobilize the ribose into the metabolism of Leishmania. To understand the catalytic role, the crystal structure of RK (LdRK) from L. donovani was determined in the apo and complex forms with several nucleotides (ATP, AMPPCP and ADP) in the presence of Na+ ion. The dual insertion of five amino acid stretches makes LdRK structurally unique from other reported structures of RKs. The structure of LdRK-ATP provided the basis for positioning of γ-phosphate of ATP by conserved -GAGD- motif. Liganded and unliganded structures of LdRK exists in similar conformation, which suggests binding of nucleotides does not make any significant conformational changes in nucleotide-bound structures. Substitution of a conserved asparagine with phenylalanine in ribose binding pocket differentiates the LdRK from other RKs. Glycerol molecule bound in the substrate binding pocket mimics the enzyme-substrate interactions but in turn, hampers the binding of ribose to LdRK. Comparative structural analysis revealed the flexibility of γ-phosphate, which adopts multiple conformations in the absence of divalent metal ion and ribose. Similar to other RKs, LdRK is also dependent on monovalent as well as divalent cations for its catalytic activity.
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Affiliation(s)
- Santhosh Gatreddi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Vijaykumar Pillalamarri
- CSIR-Indian Institute of Chemical Technology, Applied Biology, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | | | - Anthony Addlagatta
- CSIR-Indian Institute of Chemical Technology, Applied Biology, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India.
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