Discovery of PPi-type Phosphoenolpyruvate Carboxykinase Genes in Eukaryotes and Bacteria

Chiba, Yoko; Kamikawa, Ryoma; Nakada‐Tsukui, Kumiko; Saito‐Nakano, Yumiko; Nozaki, Tomoyoshi

doi:10.1074/jbc.m115.672907

Cited by 41 publications

(35 citation statements)

References 48 publications

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“…The evolutional trajectory of the PPi-dependent kinases is a controversial topic. For example, three hypotheses of the evolutional relationship between PPi-PFK and ATP-PFK have been proposed: PPi-PFK evolved into or from ATP-PFK 5 , 6 , 11 or emerged from a common ancestor independently of ATP-PFK 36 . In the ribokinase family, the evolutional trace has been discussed based on the size of the lid domain 37 , which covers the ligand-binding site.…”

Section: Discussionmentioning

confidence: 99%

“…A few kinases utilize atypical donors other than ATP. One utilizes ADP as the donor 1 – 4 , another uses inorganic pyrophosphate (PPi) 5 – 7 , and enzymes that utilize inorganic polyphosphate are also known 8 , 9 . The mechanism governing donor specificity and the evolutional trajectory of these unique enzymes have been widely discussed but are still unclear 1 ,5, 6 , 8 – 12 .…”

Section: Introductionmentioning

confidence: 99%

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Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants

et al. 2018

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Almost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants

et al. 2018

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“…However, three separate enzymes also allow for carbon fixation to produce oxaloacetate and may promote the production of succinate. Two separate PEP carboxykinases were identified: a GTP-dependent variant (4.1.1.32) found only in P. propionicum and a recently sequenced polyphosphate-dependent variant [ 85 ] found in all propionibacteria studied. Both P. acidipropionici and P. propionicum contained an additional pyruvate carboxylase (6.4.1.1).…”

Section: Resultsmentioning

confidence: 99%

A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity

McCubbin

Gonzalez-Garcia

Palfreyman

et al. 2020

Genes

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Propionibacteria have been studied extensively since the early 1930s due to their relevance to industry and importance as human pathogens. Still, their unique metabolism is far from fully understood. This is partly due to their signature high GC content, which has previously hampered the acquisition of quality sequence data, the accurate annotation of the available genomes, and the functional characterization of genes. The recent completion of the genome sequences for several species has led researchers to reassess the taxonomical classification of the genus Propionibacterium, which has been divided into several new genres. Such data also enable a comparative genomic approach to annotation and provide a new opportunity to revisit our understanding of their metabolism. Using pan-genome analysis combined with the reconstruction of the first high-quality Propionibacterium genome-scale metabolic model and a pan-metabolic model of current and former members of the genus Propionibacterium, we demonstrate that despite sharing unique metabolic traits, these organisms have an unexpected diversity in central carbon metabolism and a hidden layer of metabolic complexity. This combined approach gave us new insights into the evolution of Propionibacterium metabolism and led us to propose a novel, putative ferredoxin-linked energy conservation strategy. The pan-genomic approach highlighted key differences in Propionibacterium metabolism that reflect adaptation to their environment. Results were mathematically captured in genome-scale metabolic reconstructions that can be used to further explore metabolism using metabolic modeling techniques. Overall, the data provide a platform to explore Propionibacterium metabolism and a tool for the rational design of strains.

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“…Phosphoenolpyruvate (PEP) is a metabolic hub that connects various pathways, including glycolysis, gluconeogenesis, and metabolism of organic and amino acids (Chiba et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Among the enzymes that metabolize PEP, PEPCK is particularly relevant, due to its numerous physiological functions (Leegood and Walker, 2003;Latorre-Muro et al, 2018;Wang and Dong, 2019). Based on the phosphate donor, PEPCKs are classified as ATP-(EC 4.1.1.49), GTP-(EC 4.1.1.32) or PPi-dependent (EC 4.1.1.38), all with different evolutionary origin (Matte et al, 1997;Fukuda et al, 2004;Aich and Delbaere, 2007;Chiba et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Proteolytic cleavage ofArabidopsis thalianaphosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation

Rojas

Hartman

Figueroa

et al. 2020

Preprint

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Phosphoenolpyruvate carboxykinase (PEPCK) plays a crucial role in gluconeogenesis. In this work, we analyze the proteolysis of Arabidopsis thaliana PEPCK1 (AthPEPCK1) in germinating seedlings. We found that expression of AthPEPCK1 peaks at 24-48 hours post-imbibition. Concomitantly, we observed shorter versions of AthPEPCK1, putatively generated by metacaspase-9 (AthMC9). To study the impact of AthMC9 cleavage on the kinetic and regulatory properties of AthPEPCK1, we produced truncated mutants based on the reported AthMC9 cleavage sites. The Δ19 and Δ101 truncated mutants of AthPEPCK1 showed similar kinetic parameters and the same quaternary structure than the WT. However, activation by malate and inhibition by glucose 6-phosphate were abolished in the Δ101 mutant. We propose that proteolysis of AthPEPCK1 in germinating seedlings operates as a mechanism to adapt the sensitivity to allosteric regulation during the sink-to-source transition.HighlightThis paper describes the effects of the N-terminal proteolytic cleavage on the kinetic and regulatory properties of Arabidopsis thaliana phosphoenolpyruvate carboxykinase-1.

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Discovery of PPi-type Phosphoenolpyruvate Carboxykinase Genes in Eukaryotes and Bacteria

Cited by 41 publications

References 48 publications

Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants

Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants

A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity

Proteolytic cleavage ofArabidopsis thalianaphosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation

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