Activation of spinach pullulanase by reduction results in a decrease in the number of isomeric forms

Turning the Knobs: The Impact of Post-translational Modifications on Carbon Metabolism

Plants rely on the carbon fixed by photosynthesis into sugars to grow and reproduce. However, plants often face non-ideal conditions caused by biotic and abiotic stresses. These constraints impose challenges to managing sugars, the most valuable plant asset. Hence, the precise management of sugars is crucial to avoid starvation under adverse conditions and sustain growth. This review explores the role of post-translational modifications (PTMs) in the modulation of carbon metabolism. PTMs consist of chemical modifications of proteins that change protein properties, including protein-protein interaction preferences, enzymatic activity, stability, and subcellular localization. We provide a holistic view of how PTMs tune resource distribution among different physiological processes to optimize plant fitness.

NTRC and Thioredoxin f Overexpression Differentially Induces Starch Accumulation in Tobacco Leaves

Thioredoxin (Trx) f and NADPH-dependent Trx reductase C (NTRC) have both been proposed as major redox regulators of starch metabolism in chloroplasts. However, little is known regarding the specific role of each protein in this complex mechanism. To shed light on this point, tobacco plants that were genetically engineered to overexpress the NTRC protein from the chloroplast genome were obtained and compared to previously generated Trx f-overexpressing transplastomic plants. Likewise, we investigated the impact of NTRC and Trx f deficiency on starch metabolism by generating Nicotiana benthamiana plants that were silenced for each gene. Our results demonstrated that NTRC overexpression induced enhanced starch accumulation in tobacco leaves, as occurred with Trx f. However, only Trx f silencing leads to a significant decrease in the leaf starch content. Quantitative analysis of enzyme activities related to starch synthesis and degradation were determined in all of the genotypes. Zymographic analyses were additionally performed to compare the amylolytic enzyme profiles of both transplastomic tobacco plants. Our findings indicated that NTRC overexpression promotes the accumulation of transitory leaf starch as a consequence of a diminished starch turnover during the dark period, which seems to be related to a significant reductive activation of ADP-glucose pyrophosphorylase and/or a deactivation of a putative debranching enzyme. On the other hand, increased starch content in Trx f-overexpressing plants was connected to an increase in the capacity of soluble starch synthases during the light period. Taken together, these results suggest that NTRC and the ferredoxin/Trx system play distinct roles in starch turnover.

New insights into redox control of starch degradation

Starch is one of the major sinks of fixed carbon in photosynthetic tissues of higher plants. Carbon fixation and the synthesis of primary starch occur during the day in the chloroplast stroma, whereas starch degradation typically occurs during the following night to fuel the whole plant with energy and carbon in the absence of photosynthesis. Redox-based regulatory systems play a central role in the modulation of several chloroplastic pathways. Reversible oxidations of cysteine residues are post-translational modifications that orchestrate the precise functioning of chloroplast pathways together with changes in pH, Mg(2+) and concentrations of metabolic intermediates. Leaf starch metabolism has been intensively studied. The enzymes involved in starch synthesis and degradation have been identified and characterized. However, the redox control of the enzymes responsible for starch degradation at night remains elusive, and their response to redox transitions conflicts with the timing of the physiological events. Most of the enzymes of starch degradation are activated by reducing conditions, characteristic of daytime. Thus, redox control may have only a minor role during starch degradation at night, but could become relevant for daily stomatal opening in guard cells or in the re-allocation of fixed carbon in mesophyll cells in response to stress conditions.

Metabolic control of redox and redox control of metabolism in plants

SIGNIFICANCE

Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression.

RECENT ADVANCES

The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels.

CRITICAL ISSUES

It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels.

FUTURE DIRECTIONS

Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.

Comprehensive survey of redox sensitive starch metabolising enzymes in Arabidopsis thaliana

In chloroplasts, the ferredoxin/thioredoxin pathway regulates enzyme activity in response to light by reduction of regulatory disulfides in target enzymes, ensuring coordination between photosynthesis and diurnal metabolism. Although earlier studies have suggested that many starch metabolic enzymes are similarly regulated, redox regulation has only been verified for a few of these in vitro. Using zymograms and enzyme assays, we performed a comprehensive analysis of the redox sensitivity of known starch metabolising enzymes in extracts of Arabidopsis thaliana. Manipulation of redox potentials revealed that several enzymatic activities where activated by reduction at physiologically relevant potentials. Among these where the isoamylase complex AtISA1/AtISA2, the limit dextrinase AtLDA, starch synthases AtSS1 and AtSS3, and the starch branching enzyme AtBE2. The reversibility of the redox reaction was confirmed by enzyme assays for AtLDA, AtSS1 and AtSS3. Analysis of an AtBAM1 knock-out mutant identified an additional redox sensitive β-amylase activity, which was most likely AtBAM3. A similar requirement for reducing conditions was observed for recombinant chloroplastic α-amylase (AtAMY3) activity. This study adds further candidates to the list of reductively activated starch metabolising enzymes and supports the view that redox regulation plays a role in starch metabolism.

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

BACKGROUND

Starch serves as a temporal storage of carbohydrates in plant leaves during day/night cycles. To study transcriptional regulatory modules of this dynamic metabolic process, we conducted gene regulation network analysis based on small-sample inference of graphical Gaussian model (GGM).

RESULTS

Time-series significant analysis was applied for Arabidopsis leaf transcriptome data to obtain a set of genes that are highly regulated under a diurnal cycle. A total of 1,480 diurnally regulated genes included 21 starch metabolic enzymes, 6 clock-associated genes, and 106 transcription factors (TF). A starch-clock-TF gene regulation network comprising 117 nodes and 266 edges was constructed by GGM from these 133 significant genes that are potentially related to the diurnal control of starch metabolism. From this network, we found that β-amylase 3 (b-amy3: At4g17090), which participates in starch degradation in chloroplast, is the most frequently connected gene (a hub gene). The robustness of gene-to-gene regulatory network was further analyzed by TF binding site prediction and by evaluating global co-expression of TFs and target starch metabolic enzymes. As a result, two TFs, indeterminate domain 5 (AtIDD5: At2g02070) and constans-like (COL: At2g21320), were identified as positive regulators of starch synthase 4 (SS4: At4g18240). The inference model of AtIDD5-dependent positive regulation of SS4 gene expression was experimentally supported by decreased SS4 mRNA accumulation in Atidd5 mutant plants during the light period of both short and long day conditions. COL was also shown to positively control SS4 mRNA accumulation. Furthermore, the knockout of AtIDD5 and COL led to deformation of chloroplast and its contained starch granules. This deformity also affected the number of starch granules per chloroplast, which increased significantly in both knockout mutant lines.

CONCLUSIONS

In this study, we utilized a systematic approach of microarray analysis to discover the transcriptional regulatory network of starch metabolism in Arabidopsis leaves. With this inference method, the starch regulatory network of Arabidopsis was found to be strongly associated with clock genes and TFs, of which AtIDD5 and COL were evidenced to control SS4 gene expression and starch granule formation in chloroplasts.

Redox regulation of carbon storage and partitioning in response to light and sugars

Redox signals generated by the photosynthetic electron transport chain are known to be involved in regulating the Calvin cycle, ATP synthesis, and NADPH export from chloroplasts in response to light. The signal cascade involves transfer of electrons from photosystem I via the ferredoxin-thioredoxin system to target enzymes that are activated by reduction of regulatory disulphide bonds. The purpose of this review is to discuss recent findings showing that this concept can be extended to the regulation of carbon storage and partitioning in plants. Starch is the major carbon store in plants, and ADP-glucose pyrophosphorylase (AGPase) is the key regulatory enzyme of starch synthesis in the plastid. It has been shown that AGPase from potato tubers is subject to post-translational redox modification, and here experimental data will be provided showing that the isozyme from pea leaf chloroplasts is activated by reduced thioredoxin f or m in a similar way. Recent reports will be summarized providing in planta evidence that this mechanism regulates storage starch synthesis in response to light and sugars. Post-translational redox activation of AGPase in response to sugars is part of a signalling mechanism linking the rate of starch synthesis to the availability of carbon in diverse plant tissues. Some of the components of the signalling pathway reporting changes in the cytosolic sugar status to the plastid have been postulated, but detailed work is in progress to confirm the exact mode of action. Recent evidence will be discussed showing that key enzymes of de novo fatty acid synthesis (acetyl-CoA carboxylase) and ammonium assimilation (glutamine synthetase and glutamine:oxoglutarate amino transferase) are regulated by reversible disulphide-bond formation similar to AGPase. Redox regulation is proposed to be the preferred strategy of plastidial enzymes to regulate various metabolic processes such as carbon fixation, starch metabolism, lipid synthesis, and amino acid synthesis in response to physiological and environmental inputs.

From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule

Plants, green algae, and cyanobacteria synthesize storage polysaccharides by a similar ADPglucose-based pathway. Plant starch metabolism can be distinguished from that of bacterial glycogen by the presence of multiple forms of enzyme activities for each step of the pathway. This multiplicity does not coincide with any functional redundancy, as each form has seemingly acquired a distinctive and conserved role in starch metabolism. Comparisons of phenotypes generated by debranching enzyme-defective mutants in Escherichia coli and plants suggest that enzymes previously thought to be involved in polysaccharide degradation have been recruited during evolution to serve a particular purpose in starch biosynthesis. Speculations have been made that link this recruitment to the appearance of semicrystalline starch in photosynthetic eukaryotes. Besides the common core pathway, other enzymes of malto-oligosaccharide metabolism are required for normal starch metabolism. However, according to the genetic and physiological system under study, these enzymes may have acquired distinctive roles.

Identification of polysaccharide binding proteins by affinity electrophoresis in inhomogeneous polyacrylamide gels and subsequent SDS-PAGE/matrix-assisted laser desorption ionization-time of flight analysis

A procedure that allows the identification of polysaccharide binding polypeptides is described. The method can be applied to proteins whose enzymatic activity is either unknown or cannot be identified unambiguously by activity-staining procedures and it has been used for very complex protein mixtures, such as crude extracts of plant organs. The procedure consists of three steps. First, an affinity polyacrylamide gel electrophoresis using an inhomogeneous polyacrylamide slab gel composed of two triangular parts, an upper gel lacking the ligand and a lower triangular gel containing an immobilized ligand, is performed. Proteins that interact with the ligand form bands that deviate from those of nonbinding proteins and can be detected by protein staining (or, if possible, by activity staining). Second, the bands containing the interacting proteins are excised, denatured, and subjected to SDS-PAGE using a slab gel. In the resulting protein pattern the target proteins cover most of the length of the gel piece applied to the SDS gel, whereas contaminating proteins appear as spots or narrow bands. Suitable regions of the target protein bands are selected for tryptic digestion. Third, the resulting peptides are analyzed by matrix-assisted laser desorption ionization-mass spectrometry followed by database research.