Dichotomic Phylogenetic Tree of the Pyruvate Kinase Family

Oria-Hernández, Jesús; Riveros‐Rosas, Héctor; Ramírez‐Silva, Leticia

doi:10.1074/jbc.m605310200

Cited by 32 publications

(61 citation statements)

References 61 publications

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“…The binding site for K in PK has been identified and is well conserved in most eukaryotic PK isoforms, including all Arabidopsis isoforms apart from one that is exclusively expressed in pollen (Schmid et al, 2005;Oria-Hernandez et al, 2006). Rabbit muscle PK shows a 10,000-fold increase of in vitro activity when K is present The response is better described with the Hill model than with Michaelis-Menten kinetics (Ramirez-Silva and Oria-Hernandez, 2003).…”

Section: Allosteric and Direct Effects Of Kmentioning

confidence: 93%

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Multilevel Analysis of Primary Metabolism Provides New Insights into the Role of Potassium Nutrition for Glycolysis and Nitrogen Assimilation in Arabidopsis Roots

et al. 2009

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Potassium (K) is required in large quantities by growing crops, but faced with high fertilizer prices, farmers often neglect K application in favor of nitrogen and phosphorus. As a result, large areas of farmland are now depleted of K. K deficiency affects the metabolite content of crops with negative consequences for nutritional quality, mechanical stability, and pathogen/ pest resistance. Known functions of K in solute transport, protein synthesis, and enzyme activation point to a close relationship between K and metabolism, but it is unclear which of these are the most critical ones and should be targeted in biotechnological efforts to improve K usage efficiency. To identify metabolic targets and signaling components of K stress, we adopted a multilevel approach combining transcript profiles with enzyme activities and metabolite profiles of Arabidopsis (Arabidopsis thaliana) plants subjected to low K and K resupply. Roots and shoots were analyzed separately. Our results show that regulation of enzymes at the level of transcripts and proteins is likely to play an important role in plant adaptation to K deficiency by (1) maintaining carbon flux into amino acids and proteins, (2) decreasing negative metabolic charge, and (3) increasing the nitrogen-carbon ratio in amino acids. However, changes in transcripts and enzyme activities do not explain the strong and reversible depletion of pyruvate and accumulation of sugars observed in the roots of low-K plants. We propose that the primary cause of metabolic disorders in low-K plants resides in the direct inhibition of pyruvate kinase activity by low cytoplasmic K in root cells.

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Section: Allosteric and Direct Effects Of Kmentioning

confidence: 93%

“…In this context, it is interesting that many prokaryotic PKs lack a K-binding site and are K independent (Oria-Hernandez et al, 2006). Overexpression of a K-independent bacterial PK in Arabidopsis could be one way to test our hypothesis.…”

Section: Allosteric and Direct Effects Of Kmentioning

confidence: 99%

Multilevel Analysis of Primary Metabolism Provides New Insights into the Role of Potassium Nutrition for Glycolysis and Nitrogen Assimilation in Arabidopsis Roots

et al. 2009

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“…tenax enzyme exhibited positive cooperativity toward PEP and Mg 2ϩ . From phylogenetic analyses, it has been concluded that the PK family is subdivided into two distinct branches (232,235,236), and it appears that this clustering is due to K ϩ dependence or independence (236). The archaeal PK sequences show a high degree of similarity with their bacterial and eukaryotic counterparts, including the prosite consensus patterns for PKs (232,235).…”

Section: Phosphoenolpyruvate Conversion To Pyruvatementioning

confidence: 99%

“…acidophilum enzyme, archaeal PKs do not depend on the presence of monovalent cations like K ϩ or NH 4 ϩ , as described for many other PKs from Bacteria and Eukarya. This independence was attributed to the substitution of a conserved glutamate, which is highly conserved in the K ϩ sites of PKs stimulated by monovalent cations (232,236). This glutamate is also present in the K ϩ -dependent Tpl.…”

Section: Phosphoenolpyruvate Conversion To Pyruvatementioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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“…For example, although there are common organizational principles in diverse regulatory, signal-transduction, and metabolic pathways, dramatic cases of rewiring have been revealed with the expansion of molecular and cell biological investigations to multiple species. Such examples include aspects of mating-type specification (14,15), meiosis (16), cell cycle (17, 18), biosynthetic pathways (19)(20)(21)(22)(23), protein transport (24), nuclear organization (25), and ribosome production (26,27). These kinds of observations imply that there are often numerous degrees of freedom for reorganizing the underlying determinants of otherwise constant cellular processes.…”

mentioning

confidence: 99%

Evolutionary cell biology: Two origins, one objective

Lynch

Field

Goodson

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

111

115

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All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within-and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.evolutionary cell biology | cell biology | adaptive evolution | random genetic drift | cellular evolutionThe origin of cells constituted one of life's most important early evolutionary transitions, simultaneously enabling replicating entities to corral the fruits of their catalytic labor and providing a unit of inheritance necessary for further evolutionary refinement and diversification. The centrality of cellular features to all aspects of biology motivates the focus of cell biology on the biophysical/biochemical aspects of a broad swath of traits that include gene expression, metabolism, intracellular transport and communication, cellcell interactions, locomotion, and growth. No one questions the rich contributions that have resulted from this focus on how cells work. However, with an emphasis on maximizing experimental consistency in a few well-characterized model systems, cell biologists have generally eschewed the variation that motivates most questions in evolutionary biology.Because all evolutionary change ultimately requires modifications at the cellular level, questioning and understanding how cellular features arise and diversify should be a central research venue in evolutionary biology. However, if there is one glaring gap in this field, it is the absence of widespread cell-biological thinking. Despite the surge of interest at the molecular, genomic, and developmental levels, much of today's study of evolution is only moderately concerned with cellular features, perhaps due to lack of appreciation for...

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Dichotomic Phylogenetic Tree of the Pyruvate Kinase Family

Cited by 32 publications

References 61 publications

Multilevel Analysis of Primary Metabolism Provides New Insights into the Role of Potassium Nutrition for Glycolysis and Nitrogen Assimilation in Arabidopsis Roots

Multilevel Analysis of Primary Metabolism Provides New Insights into the Role of Potassium Nutrition for Glycolysis and Nitrogen Assimilation in Arabidopsis Roots

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Evolutionary cell biology: Two origins, one objective

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