Molecular, Kinetic, and Immunological Properties of the 6-Phosphofructokinase from the Green Alga Selenastrum minutum: Activation during Biosynthetic Carbon Flow

Structure function analysis of ADP-dependent cyanobacterial phosphofructokinase reveals new phylogenetic grouping in the PFK-A family

Depending on the light conditions, photosynthetic organisms switch between carbohydrate synthesis or breakdown, for which the reversibility of carbohydrate metabolism, including glycolysis, is essential. Kinetic regulation of phosphofructokinase (PFK), a key-control point in glycolysis, was studied in the cyanobacterium Synechocystis sp. PCC 6803. The two PFK iso-enzymes (PFK- A1, PFK-A2), were found to use ADP instead of ATP, and have similar kinetic characteristics, but differ in their allosteric regulation. PFK-A1 is inhibited by 3-phosphoglycerate, a product of the Calvin-Benson-Bassham cycle, while PFK-A2 is inhibited by ATP, which is provided by photosynthesis. This regulation enables cyanobacteria to switch PFK off in light, and on in darkness. ADP dependence has not been reported before for the PFK-A enzyme family and was thought to be restricted to the PFK-B ribokinase superfamily. Phosphate donor specificity within the PFK-A family could be related to specific binding motifs in ATP-, ADP-, and PPi-dependent PFK-As. Phylogenetic analysis revealed a distribution of ADP-PFK-As in cyanobacteria and in a few alphaproteobacteria, which was confirmed in enzymatic studies.

Response mechanism of harmful algae Phaeocystis globosa to ocean warming and acidification

Simultaneous ocean warming and acidification will alter marine ecosystem structure and directly affect marine organisms. The alga Phaeocystis globosa commonly causes harmful algal blooms in coastal areas of eastern China. P. globosa often outcompetes other species due to its heterotypic life cycle, primarily including colonies and various types of solitary cells. However, little is known about the adaptive response of P. globosa to ocean warming and acidification. This study aimed to reveal the global molecular regulatory networks implicated in the response of P. globosa to simultaneous warming and acidification. After exposure to warming and acidification, the phosphatidylinositol (PI) and mitogen-activated protein kinase (MAPK) signaling pathways of P. globosa were activated to regulate other molecular pathways in the cell, while the light harvesting complex (LHC) genes were downregulated to decrease photosynthesis. Exposure to warming and acidification also altered the intracellular energy flow, with more energy allocated to the TCA cycle rather than to the biosynthesis of fatty acids and hemolytic substances. The upregulation of genes associated with glycosaminoglycan (GAG) degradation prevented the accumulation of polysaccharides, which led to a reduction in colony formation. Finally, the upregulation of the Mre11 and Rad50 genes in response to warming and acidification implied an increase in meiosis, which may be used by P. globosa to increase the number of solitary cells. The increase in genetic diversity through sexual reproduction may be a strategy of P. globosa that supports rapid response to complex environments. Thus, the life cycle of P. globosa underwent a transition from colonies to solitary cells in response to warming and acidification, suggesting that this species may be able to rapidly adapt to future climate changes through life cycle transitions.

Transcriptomic responses to phosphorus in an invasive cyanobacterium, Raphidiopsis raciborskii: Implications for nutrient management

Phosphorus (P) is a vital macronutrient associated with the growth and proliferation of Raphidiopsis raciborskii, an invasive and notorious bloom-forming cyanobacterium. However, the molecular mechanisms involved in P acclimation remain largely unexplored for Raphidiopsis raciborskii. Here, transcriptome sequencing of Raphidiopsis raciborskii was conducted to reveal multifaceted mechanisms involved in mimicking dipotassium phosphate (DIP), β-glycerol phosphate (Gly), 2-aminoethylphosphonic acid (AEP), and P-free conditions (NP). Chlorophyll a fluorescence parameters showed significant differences in the NP and AEP groups compared with the DIP and Gly-groups. Expression levels of genes related to phosphate transportation and uptake, organic P utilization, nitrogen metabolism, urea cycling, carbon fixation, amino acid metabolism, environmental information, the ATP-synthesis process in glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway were remarkably upregulated, while those related to photosynthesis, phycobiliproteins, respiration, oxidative phosphorylation, sulfur metabolism, and genetic information were markedly downregulated in the NP group relative to the DIP group. However, the expression of genes involved in organic P utilization, the urea cycle, and genetic information in the Gly-group, and carbon-phosphorus lyase, genetic information and environmental information in the AEP group were significantly increased compared to the DIP group. Together, these results indicate that Raphidiopsis raciborskii exhibits the evolution of coordination of multiple metabolic pathways and certain key genes to adapt to ambient P changes, which implies that if P is reduced to control Raphidiopsis raciborskii bloom, there is a risk that external nutrients (such as nitrogen, amino acids, and urea) will stimulate the growth or metabolism of Raphidiopsis.

Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate

Although gene regulation can occur at both transcriptional and epigenetic (microRNA) levels, combined transcriptomic and microRNAomic responses to environmental stress are still largely unexplored for marine plankton. Here, we conducted transcriptome and microRNAome sequencing for Prorocentrum donghaiense to understand the molecular mechanisms by which this dinoflagellate copes with phosphorus (P) deficiency. Under P-depleted conditions, G1/S specific cyclin gene was markedly downregulated, consistent with growth inhibition, and genes related to dissolved organic phosphorus (DOP) hydrolysis, carbon fixation, nitrate assimilation, glycolysis, and cellular motility were upregulated. The elevated expression of ATP-generating genes (for example, rhodopsin) and ATP-consuming genes suggests some metabolic reconfiguration towards accelerated ATP recycling under P deficiency. MicroRNAome sequencing revealed 17 microRNAs, potentially regulating 3268 protein-coding genes. Functional enrichment analysis of these microRNA-targeted genes predicted decreases in sulfatide (sulfolipid) catabolism under P deficiency. Strikingly, we detected a significant increase in sulfolipid sulfatide content (but not in sulphoquinovosyldiacylglycerol content) and its biosynthesis gene expression, indicating a different sulfolipid-substituting-phospholipid mechanism in this dinoflagellate than other phytoplankters studied previously. Taken together, our integrative transcriptomic and microRNAomic analyses show that enhanced DOP utilization, accelerated ATP cycling and repressed sulfolipid degradation constitute a comprehensive strategy to cope with P deficiency in a model dinoflagellate.

Characterisation of the ATP-dependent phosphofructokinase gene family from Arabidopsis thaliana

Plants possess two different types of phosphofructokinases, an ATP-dependent (PFK) and a pyrophosphate-dependent form (PFP). While plant PFPs have been investigated in detail, cDNA clones coding for PFK have not been identified in Arabidopsis thaliana. Searching the A. thaliana genome revealed 11 putative members of a phosphofructokinase gene family. Among those, four sequences showed high homology to the alpha- or beta-subunits of plant PFPs. Seven cDNAs resulted in elevated PFK, but not PFP activity after transient expression in tobacco leaves suggesting that they encode Arabidopsis PFKs. RT-PCR revealed different tissue-specific expression of the individual forms. Furthermore, analysis of GFP fusion proteins indicated their presence in different sub-cellular compartments.

Purification, microsequencing and cloning of spinach ATP-dependent phosphofructokinase link sequence and function for the plant enzyme

Despite its importance in plant metabolism, no sequences of higher plant ATP-dependent phosphofructokinase (EC 2.7.1.11) are annotated in the databases. We have purified the enzyme from spinach leaves 309-fold to electrophoretic homogeneity. The purified enzyme was a homotetramer of approximately 52 kDa subunits with a specific activity of 600 mU x mg(-1) and a Km value for ATP of 81 microm. The purified enzyme was not activated by phosphate, but slightly inhibited instead, suggesting that it was the chloroplast isoform. The inclusion of adenosine 5'-(beta,gamma-imido)triphosphate was conducive to enzyme activity during the purification protocol. The sequences of eight tryptic peptides from the final protein preparation, which did not utilize pyrophosphate as a phosphoryl donor, were determined and an exactly corresponding cDNA was cloned. The sequence of enzymatically active spinach ATP-dependent phosphofructokinase suggests that a large family of genomics-derived higher plant sequences currently annotated in the databases as putative pyrophosphate-dependent phosphofructokinases according to sequence similarity is misannotated with respect to the cosubstrate.

THE ORGANIZATION AND REGULATION OF PLANT GLYCOLYSIS

This review discusses the organization and regulation of the glycolytic pathway in plants and compares and contrasts plant and nonplant glycolysis. Plant glycolysis exists both in the cytosol and plastid, and the parallel reactions are catalyzed by distinct nuclear-encoded isozymes. Cytosolic glycolysis is a complex network containing alternative enzymatic reactions. Two alternate cytosolic reactions enhance the pathway's ATP yield through the use of pyrophosphate in place of ATP. The cytosolic glycolytic network may provide an essential metabolic flexibility that facilitates plant development and acclimation to environmental stress. The regulation of plant glycolytic flux is assessed, with a focus on the fine control of enzymes involved in the metabolism of fructose-6-phosphate and phosphoenolpyruvate. Plant and nonplant glycolysis are regulated from the "bottom up" and "top down," respectively. Research on tissue- and developmental-specific isozymes of plant glycolytic enzymes is summarized. Potential pitfalls associated with studies of glycolytic enzymes are considered. Some glycolytic enzymes may be multifunctional proteins involved in processes other than carbohydrate metabolism.

Activation of Respiration to Support Dark NO(3) and NH(4) Assimilation in the Green Alga Selenastrum minutum

Short-term changes in pyridine nucleotides and other key metabolites were measured during the onset of NO(3) (-) or NH(4) (+) assimilation in the dark by the N-limited green alga Selenastrum minutum. When NH(4) (+) was added to N-limited cells, the NADH/NAD ratio rose immediately and the NADPH/NADP ratio followed more slowly. An immediate decrease in glutamate and 2-oxoglutarate indicates an increased flux through the glutamine synthase/glutamate oxoglutarate aminotransferase. Pyruvate kinase and phosphoenolpyruvate carboxylase are rapidly activated to supply carbon skeletons to the tricarboxylic acid cycle for amino acid synthesis. In contrast, NO(3) (-) addition caused an immediate decrease in the NADPH/NADP ratio that was accompanied by an increase in 6-phosphogluconate and decrease in the glucose-6-phosphate/6-phosphogluconate ratio. These changes show increased glucose-6-phosphate dehydrogenase activity, indicating that the oxidative pentose phosphate pathway supplies some reductant for NO(3) (-) assimilation in the dark. A lag of 30 to 60 seconds in the increase of the NADH/NAD ratio during NO(3) (-) assimilation correlates with a slow activation of pyruvate kinase and phosphoenolpyruvate carboxylase. Together, these results indicate that during NH(4) (+) assimilation, the demand for ATP and carbon skeletons to synthesize amino acid signals activation of respiratory carbon flow. In contrast, during NO(3) (-) assimilation, the initial demand on carbon respiration is for reductant and there is a lag before tricarboxylic acid cycle carbon flow is activated in response to the carbon demands of amino acid synthesis.

Effects of Phosphorus Limitation on Respiratory Metabolism in the Green Alga Selenastrum minutum

The effects of phosphorus nutrition on several physiological and biochemical parameters of the green alga, Selenastrum minutum, have been examined. Algal cells were cultured in chemostats under conditions of either Pi limitation or nutrient sufficiency. Pi limitation resulted in: (a) a 5-fold lower rate of respiration, (b) a 3-fold decline in rates of photosynthetic carbon dioxide fixation and oxygen evolution, (c) a 3-fold higher rate of dark carbon dioxide fixation, (d) significant increases in activities of phosphoenolpyruvate (PEP) carboxylase and PEP phosphatase (128% and 158% of nutrient sufficient activities, respectively), (e) significant reductions in activities of nonphosphorylating NADP-glyceraldehyde-3-phosphate dehydrogenase and NAD malic enzyme, and (f) no change in levels of ATP:fructose-6-phosphate 1-phosphotransferase, phosphorylating NAD-glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and pyruvate kinase. The intracellular concentrations of Pi, ATP, AMP, soluble protein, and chlorophyll were also significantly reduced in response to Pi limitation. As well, the level of ADP was about 11-fold lower in the Pi-limited cells as compared to the nutrient sufficient controls. It was predicted that because of this low level of ADP, pyruvate kinase catalyzed conversion of PEP to pyruvate may be restricted in Pi-limited cells. During Pi limitation, PEP carboxylase and PEP phosphatase may function to "bypass" the ADP dependent pyruvate kinase, as well as to recycle Pi for its reassimilation into cellular metabolism.

Anaerobic Metabolism in the N-Limited Green Alga Selenastrum minutum: II. Assimilation of Ammonium by Anaerobic Cells

The green alga Selenastrum minutum (Naeg.) Collins is able to assimilate NH(4) (+) in the dark under anaerobic conditions (GC Vanlerberghe, AK Horsey, HG Weger, DH Turpin [1989] Plant Physiol 91: 1551-1557). In the present study, analysis of metabolites following addition of NH(4) (+) to cells acclimated to anaerobic conditions has shown the following. There was a transient decline in adenylate energy charge from 0.6 to 0.4 followed by a recovery back to ~0.6. This was accompanied by a rapid increase in pyruvate/phosphoenolpyruvate and fructose-1,6-bisphosphate/fructose-6-phosphate ratios indicating activation of pyruvate kinase and 6-phosphofructokinase, respectively. There was also an increase in fructose-2,6-bisphosphate, which, since this alga lacks pyrophosphate dependent 6-phosphofructokinase can be inferred to inhibit gluconeogenic fructose-1,6-bisphosphatase. These changes resulted in an increase in the rate of anaerobic starch breakdown. Anaerobic NH(4) (+) assimilation also resulted in a two-fold increase in the rate of production of the major fermentative end-products in this alga, d-lactate and ethanol. There was no change in the rate of accumulation of the fermentative end product succinate but malate accumulated under anoxia during NH(4) (+) assimilation. A rapid increase in Gln and decline in Glu indicates that primary NH(4) (+) assimilation under anoxia was via glutamine synthetase-glutamate synthase. Almost all N assimilated under these conditions was sequestered in alanine. These results allow us to propose a model for the regulation of carbon metabolism during anaerobic NH(4) (+) assimilation.

Anaerobic Metabolism in the N-Limited Green Alga Selenastrum minutum: I. Regulation of Carbon Metabolism and Succinate as a Fermentation Product

The onset of anaerobiosis in darkened, N-limited cells of the green alga Selenastrum minutum (Naeg.) Collins elicited the following metabolic responses. There was a rapid decrease in energy charge from 0.85 to a stable lower value of 0.6 accompanied by rapid increases in pyruvate/phosphoenolpyruvate and fructose-1,6-bisphosphate/fructose-6-phosphate ratios indicating activation of pyruvate kinase and 6-phosphofructokinase, respectively. There was also a large increase in fructose-2,6-bisphosphate, which, since this alga lacks pyrophosphate dependent 6-phosphofructokinase, can be inferred to inhibit gluconeogenic fructose-1,6-bisphosphatase activity. These changes resulted in an approximately twofold increase in the rate of starch breakdown indicating a Pasteur effect. The Pasteur effect was accompanied by accumulation of d-lactate, ethanol and succinate as fermentation end-products, but not malate. Accumulation of succinate was facilitated by reductive carbon metabolism by a partial TCA cycle (GC Vanlerberghe, AK Horsey, HG Weger, DH Turpin [1989] Plant Physiol 91: 1551-1557). An initial stoichiometric decline in aspartate and increases in succinate and alanine suggests that aspartate catabolism provides an initial source of carbon for reduction to succinate under anoxic conditions. These observations allow us to develop a model for the regulation of anaerobic carbon metabolism and a model for short-term and long-term strategies for succinate accumulation in a green alga.