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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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2
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Hwang S, Chavarria NE, Hackley RK, Schmid AK, Maupin-Furlow JA. Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen. Int J Mol Sci 2019; 20:ijms20194784. [PMID: 31561502 PMCID: PMC6801745 DOI: 10.3390/ijms20194784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H. volcanii grown on ammonium as an abundant source of fixed nitrogen compared to l-alanine, the latter of which exemplifies an intermediate source of nitrogen that can be obtained from dead cells in natural habitats. By comparing the two growth conditions, 30 genes were found to be differentially expressed, including 16 genes associated with amino acid metabolism and transport. The gene expression profiles contributed to mapping ammonium and l-alanine usage with respect to transporters and metabolic pathways. In addition, conserved DNA motifs were identified in the putative promoter regions and transcription factors were found to be in synteny with the differentially expressed genes, leading us to propose regulons of transcriptionally co-regulated operons. This study provides insight to how H. volcanii responds to and utilizes intermediate vs. abundant sources of fixed nitrogen for growth, with implications for conserved functions in related halophilic archaea.
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Affiliation(s)
- Sungmin Hwang
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | - Nikita E Chavarria
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA.
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA.
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA.
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA.
- Center for Genomics and Computational Biology, Duke University, Duke University, Durham, NC 27708, USA.
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
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Connell MB, Lee MJY, Li J, Plaxton WC, Jia Z. Structural and biochemical characterization of citrate binding to AtPPC3, a plant-type phosphoenolpyruvate carboxylase from Arabidopsis thaliana. J Struct Biol 2018; 204:507-512. [PMID: 30419358 DOI: 10.1016/j.jsb.2018.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/02/2018] [Accepted: 11/09/2018] [Indexed: 11/30/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a tightly regulated cytosolic enzyme situated at a crucial branch point of central plant metabolism. The structure of AtPPC3, a C3 PEPC isozyme of the model plant Arabidopsis thaliana, in complex with the inhibitors aspartate and citrate was solved at 2.2-Å resolution. This represents the first PEPC structure with citrate bound. Aspartate and citrate binding sites are in close proximity (5.1-5.3 Å) and interactions between citrate and specific residues were identified. Citrate functions as a mixed (allosteric) inhibitor as it reduced AtPPC3's Vmax while increasing Km(PEP) values. The PEP saturation data gave an excellent fit to the mixed inhibition model, yielding Ki and Ki' (citrate) values of 9.3 and 42.5 mM, respectively. Citrate and aspartate inhibition of AtPPC3 was non-additive, likely due to their closely positioned binding sites, their similar negative charge, and type of binding residues. Fewer interactions and lower affinity for citrate support its observed weaker inhibition of AtPPC3 relative to aspartate. Citrate does not appear to induce further conformational change beyond aspartate owing to the similar structural mechanism of inhibition. AtPPC3 largely exhibits root-specific expression in Arabidopsis, where it is markedly upregulated during stresses such as excessive salinity or nutritional Pi deprivation that necessitate large increases in anaplerotic PEP carboxylation. The cytosolic citrate concentration of potato tubers suggests that AtPPC3's inhibition by citrate may be physiologically relevant. Our results provide novel insights into the structural basis of allosteric PEPC control and the kinetic effects brought about upon inhibitor binding.
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Affiliation(s)
- Matthew B Connell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Michael J Y Lee
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Jerry Li
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - William C Plaxton
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada; Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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Shylajanaciyar M, Dineshbabu G, Rajalakshmi R, Subramanian G, Prabaharan D, Uma L. Analysis and elucidation of phosphoenolpyruvate carboxylase in cyanobacteria. Protein J 2015; 34:73-81. [PMID: 25586080 DOI: 10.1007/s10930-015-9598-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) a cytosolic enzyme of higher plants is also found in bacteria and cyanobacteria. Genetic and biochemical investigations have indicated that there are several isoforms of PEPC belonging to C3; C3/C4 and C4 groups but, the evolution of PEPC in cyanobacteria is not yet understood. The present study opens up an opportunity to understand the isoforms and functions of PEPC in cyanobacteria. The variations observed in PEPC among lower and higher orders of cyanobacteria, suggests convergent evolution of PEPC. There is a specific PEPC phosphorylation residue 'serine' at the N-terminus and PEPC determinant residue 'serine' at the C-terminal that facilitates high affinity for substrate binding. These residues were unique to higher orders of cyanobacteria, but, not in lower orders and other prokaryotes. The different PEPC forms of cyanobacteria were investigated for their kinetic properties with phosphoenolpyruvate as the substrate and the findings corroborated well with the in silico findings. In vitro enzymatic study of cyanobacteria belonging to three different orders demonstrated the role of aspartate as an allosteric effector, which inhibited PEPC by interacting with the highly conserved residues in the active site. The differences in mode of inhibition among the different order, thus, give a fair picture about the cyanobacterial PEPCs. The higher orders appear to possess the sequence coordinates and functionally conserved residues similar to isoforms of C4 type higher plants, whereas isoforms of PEPC of the lower orders did not resemble either that of C3 or C4 plants.
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Affiliation(s)
- Mohandass Shylajanaciyar
- National Facility for Marine Cyanobacteria (Sponsored by DBT, Govt. of India), Department of Marine Biotechnology, School of Marine Sciences, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
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Dharmarajan L, Kraszewski JL, Mukhopadhyay B, Dunten PW. Structure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate. Proteins 2011; 79:1820-9. [PMID: 21491491 DOI: 10.1002/prot.23006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 01/06/2011] [Accepted: 01/21/2011] [Indexed: 11/06/2022]
Abstract
The crystal structure of an archaeal-type phosphoenolpyruvate carboxylase from Clostridium perfringens has been determined based on X-ray data extending to 3 Å. The asymmetric unit of the structure includes two tetramers (each a dimer-of-dimers) of the enzyme. The precipitant, malonate, employed for the crystallization is itself a weak inhibitor of phosphoenolpyruvate carboxylase and a malonate molecule is seen in the active-site in the crystal structure. The allosteric binding sites for aspartate (an inhibitor) and glucose-6-phosphate (an activator) observed in the Escherichia coli and Zea mays phosphoenolpyruvate carboxylase structures, respectively, are not conserved in the C. perfringens structure. Aspartate inhibits the C. perfringens enzyme competitively with respect to the substrate, Mg(++.) phosphoenolpyruvate. A mechanism for inhibition is proposed based on the structure and sequence comparisons with other archaeal-type phosphoenolpyruvate carboxylases with differing sensitivity to inhibition by aspartate.
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Affiliation(s)
- Lakshmi Dharmarajan
- Virginia Bioinformatics Institute, Bioinformatics and Computational Biology Graduate Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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Peracchi A, Mozzarelli A. Exploring and exploiting allostery: Models, evolution, and drug targeting. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:922-33. [PMID: 21035570 DOI: 10.1016/j.bbapap.2010.10.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 12/11/2022]
Abstract
The concept of allostery was elaborated almost 50years ago by Monod and coworkers to provide a framework for interpreting experimental studies on the regulation of protein function. In essence, binding of a ligand at an allosteric site affects the function at a distant site exploiting protein flexibility and reshaping protein energy landscape. Both monomeric and oligomeric proteins can be allosteric. In the past decades, the behavior of allosteric systems has been analyzed in many investigations while general theoretical models and variations thereof have been steadily proposed to interpret the experimental data. Allostery has been established as a fundamental mechanism of regulation in all organisms, governing a variety of processes that range from metabolic control to receptor function and from ligand transport to cell motility. A number of studies have shed light on how evolutionary pressures have favored and molded the development of allosteric features in specific macromolecular systems. The widespread occurrence of allostery has been recently exploited for the development and design of allosteric drugs that bind to either physiological or non-physiological allosteric sites leading to gain of function or loss of function. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Alessio Peracchi
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy.
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Černý M, Doubnerová V, Müller K, Ryšlavá H. Characterization of phosphoenolpyruvate carboxylase from mature maize seeds: Properties of phosphorylated and dephosphorylated forms. Biochimie 2010; 92:1362-70. [DOI: 10.1016/j.biochi.2010.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 06/18/2010] [Indexed: 10/19/2022]
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Dharmarajan L, Kraszewski JL, Mukhopadhyay B, Dunten PW. Expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1193-6. [PMID: 19923749 DOI: 10.1107/s1744309109042663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Accepted: 10/16/2009] [Indexed: 11/10/2022]
Abstract
An archaeal-type phosphoenolpyruvate carboxylase (PepcA) from Clostridium perfringens has been expressed in Escherichia coli in a soluble form with an amino-terminal His tag. The recombinant protein is enzymatically active and two crystal forms have been obtained. Complete diffraction data extending to 3.13 angstrom resolution have been measured from a crystal soaked in KAu(CN)(2), using radiation at a wavelength just above the Au L(III) edge. The asymmetric unit contains two tetramers of PepcA.
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Bolanos-Garcia VM, Fernandez-Recio J, Allende JE, Blundell TL. Identifying interaction motifs in CK2beta--a ubiquitous kinase regulatory subunit. Trends Biochem Sci 2006; 31:654-61. [PMID: 17084631 DOI: 10.1016/j.tibs.2006.10.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/26/2006] [Accepted: 10/20/2006] [Indexed: 10/23/2022]
Abstract
Casein kinase 2 (CK2) is probably the most ubiquitous serine/threonine kinase found in eukaryotes: it phosphorylates >300 cellular proteins, ranging from transcription factors to proteins involved in chromatin structure and cell division. CK2 is a heterotetrameric enzyme that induces neoplastic growth when overexpressed. The beta subunit of CK2 (CK2beta) functions as the regulator of the catalytic CK2alpha and CK2alpha' subunits, enhancing their stability, activity and specificity. However, CK2beta also functions as a multisubstrate docking platform for several other binding partners. Here, we discuss the organization and roles of interaction motifs of CK2beta, postulate new protein-interaction sites and map these to the known interaction motifs, and show how the resulting complexity of interactions mediated by CK2 gives rise to the versatile functions of this pleiotropic protein kinase.
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