EARLY STARVATION1 specifically affects the phosphorylation action of starch‐related dikinases

Starch phosphorylation by starch‐related dikinases glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD) is a key step in starch degradation. Little information is known about the precise structure of the glucan substrate utilized by the dikinases and about the mechanisms by which these structures may be influenced. A 50‐kDa starch‐binding protein named EARLY STARVATION1 (ESV1) was analyzed regarding its impact on starch phosphorylation. In various in vitro assays, the influences of the recombinant protein ESV1 on the actions of GWD and PWD on the surfaces of native starch granules were analyzed. In addition, we included starches from various sources as well as truncated forms of GWD. ESV1 preferentially binds to highly ordered, α‐glucans, such as starch and crystalline maltodextrins. Furthermore, ESV1 specifically influences the action of GWD and PWD at the starch granule surface. Starch phosphorylation by GWD is decreased in the presence of ESV1, whereas the action of PWD increases in the presence of ESV1. The unique alterations observed in starch phosphorylation by the two dikinases are discussed in regard to altered glucan structures at the starch granule surface.     

Identification of a novel enzyme required for starch metabolism in Arabidopsis leaves. The phosphoglucan, water dikinase

The phosphorylation of amylopectin by the glucan, water dikinase (GWD; EC 2.7.9.4) is an essential step within starch metabolism. This is indicated by the starch excess phenotype of GWD-deficient plants, such as the sex1-3 mutant of Arabidopsis (Arabidopsis thaliana). To identify starch-related enzymes that rely on glucan-bound phosphate, we studied the binding of proteins extracted from Arabidopsis wild-type leaves to either phosphorylated or nonphosphorylated starch granules. Granules prepared from the sex1-3 mutant were prephosphorylated in vitro using recombinant potato (Solanum tuberosum) GWD. As a control, the unmodified, phosphate free granules were used. An as-yet uncharacterized protein was identified that preferentially binds to the phosphorylated starch. The C-terminal part of this protein exhibits similarity to that of GWD. The novel protein phosphorylates starch granules, but only following prephosphorylation with GWD. The enzyme transfers the beta-P of ATP to the phosphoglucan, whereas the gamma-P is released as orthophosphate. Therefore, the novel protein is designated as phosphoglucan, water dikinase (PWD). Unlike GWD that phosphorylates preferentially the C6 position of the glucose units, PWD phosphorylates predominantly (or exclusively) the C3 position. Western-blot analysis of protoplast and chloroplast fractions from Arabidopsis leaves reveals a plastidic location of PWD. Binding of PWD to starch granules strongly increases during net starch breakdown. Transgenic Arabidopsis plants in which the expression of PWD was reduced by either RNAi or a T-DNA insertion exhibit a starch excess phenotype. Thus, in Arabidopsis leaves starch turnover requires a close collaboration of PWD and GWD.     

The Laforin-Like Dual-Specificity Phosphatase SEX4 from Arabidopsis Hydrolyzes Both C6- and C3-Phosphate Esters Introduced by Starch-Related Dikinases and Thereby Affects Phase Transition of α-Glucans

The biochemical function of the Laforin-like dual-specific phosphatase AtSEX4 (EC 3.1.3.48) has been studied. Crystalline maltodextrins representing the A- or the B-type allomorph were prephosphorylated using recombinant glucan, water dikinase (StGWD) or the successive action of both plastidial dikinases (StGWD and AtPWD). AtSEX4 hydrolyzed carbon 6-phosphate esters from both the prephosphorylated A- and B-type allomorphs and the kinetic constants are similar. The phosphatase also acted on prelabeled carbon-3 esters from both crystalline maltodextrins. Similarly, native starch granules prelabeled in either the carbon-6 or carbon-3 position were also dephosphorylated by AtSEX4. The phosphatase did also hydrolyze phosphate esters of both prephosphorylated maltodextrins when the (phospho)glucans had been solubilized by heat treatment. Submillimolar concentrations of nonphosphorylated maltodextrins inhibited AtSEX4 provided they possessed a minimum of length and had been solubilized. As opposed to the soluble phosphomaltodextrins, the AtSEX4-mediated dephosphorylation of the insoluble substrates was incomplete and at least 50% of the phosphate esters were retained in the pelletable (phospho)glucans. The partial dephosphorylation of the insoluble glucans also strongly reduced the release of nonphosphorylated chains into solution. Presumably, this effect reflects fast structural changes that following dephosphorylation occur near the surface of the maltodextrin particles. A model is proposed defining distinct stages within the phosphorylation/dephosphorylation-dependent transition of α-glucans from the insoluble to the soluble state.The metabolism of starch, the most prominent storage carbohydrate in plants, is assumed to require approximately 30 to 40 distinct (iso)enzymes (Deschamps et al., 2008), but, presumably, the list of the starch-related proteins is not yet complete. Several novel proteins (and protein functions) essential for the normal starch metabolism have recently been identified among which are two α-glucan phosphorylating dikinases. One dikinase (glucan, water dikinase [GWD], EC 2.7.9.4) utilizes ATP as dual phosphate donor and esterifies the C6 position of amylopectin-related glucosyl residues, whereas the other dikinase (phosphoglucan, water dikinase [PWD], EC 2.7.9.5) selectively transfers the β-phosphate group from ATP to the C3 position of glucosyl residues (Ritte et al., 2006).Two other previously unknown starch-related enzymes were designated as SEX4 protein (EC 3.1.3.48; At3g52180; previous designations PTPKIS1 and DSP4) and as Like Sex Four1 (LSF1) protein (At3g01510; previously named PTPKIS2; Comparot-Moss et al., 2010). Both proteins are predicted to contain a noncatalytic carbohydrate-binding module (CBM; Boraston et al., 2004; Shoseyov et al., 2006) and a catalytic dual-specificity phosphatase (DSP) domain. The latter is shared by the large family of DSPs that dephosphorylate distinct target phosphoproteins both at phosphotyrosine and phosphoserine/phosphothreonine residues. Some DSPs also act on various nonproteinaceous substrates, such as phospholipids or phosphorylated polyglycans (Pulido and Hooft van Huijsduijnen, 2008).Arabidopsis (Arabidopsis thaliana) mutants lacking a functional SEX4 protein contain both elevated starch levels and significant amounts of soluble phosphooligoglucans that are below the limit of detection in wild-type plants and probably originate from starch. However, the precise biochemical function of SEX4 is far from being clear (Kötting et al., 2009). The phenotype of the SEX4-deficient mutant is complex: Transitory starch possesses an elevated amylose-to-amylopectin ratio but the phosphate content of amylopectin is not increased. It has been hypothesized that SEX4 and LSF1 selectively hydrolyze C6- and C3-phosphate esters, respectively, but experimental evidence is lacking (Kötting et al., 2009). Likewise, it is unknown whether SEX4 preferentially acts on particulate starch or on soluble phosphoglucans.Crystalline maltodextrins (MD_cryst) have recently been introduced as a model mimicking some structural features of the native starch granules (Hejazi et al., 2008). They can be crystallized as either the A- or the B-type allomorph (Gallant et al., 1997; Gérard et al., 2001). Recombinant StGWD phosphorylates both maltodextrin allomorphs with a far higher rate than native starch granules and thereby initiates solubilization of both phosphorylated and nonphosphorylated maltodextrins. In vitro both allomorphs act also as substrate for PWD provided a prephosphorylation by GWD (Hejazi et al., 2009).In this study, we used the prephosphorylated A- and B-type allomorphs of MD_cryst to study biochemical functions of AtSEX4. As highly ordered α-glucans are the preferred sites of the dikinase-mediated phosphorylation, we designed experiments to answer the following questions: Does SEX4 preferentially act on phosphorylated insoluble or soluble glucans? If insoluble α-glucans are the preferred substrate, does the phosphatase distinguish between the A- and the B-type allomorph? Does SEX4 preferentially or selectively hydrolyze C6-phosphate esters? Does SEX4 also interact with nonphosphorylated oligoglucans? Finally, assuming that SEX4 acts on insoluble phosphoglucans, does the removal of phosphate esters affect the phase transition and/or the physical order of the glucans?     

The plastidial glucan, water dikinase (GWD) catalyses multiple phosphotransfer reactions

The plant genome encodes at least two distinct and evolutionary conserved plastidial starch-related dikinases that phosphorylate a low percentage of glucosyl residues at the starch granule surface. Esterification of starch favours the transition of highly ordered α-glucans to a less ordered state and thereby facilitates the cleavage of interglucose bonds by hydrolases. Metabolically most important is the phosphorylation at position C6, which is catalysed by the glucan, water dikinase (GWD). The reactions mediated by recombinant wild-type GWD from Arabidopsis thaliana (AtGWD) and from Solanum tuberosum (StGWD) were studied. Two mutated proteins lacking the conserved histidine residue that is indispensible for glucan phosphorylation were also included. The wild-type GWDs consume approximately 20% more ATP than is required for glucan phosphorylation. Similarly, although incapable of phosphorylating α-glucans, the two mutated dikinase proteins are capable of degrading ATP. Thus, consumption of ATP and phosphorylation of α-glucans are not strictly coupled processes but, to some extent, occur as independent phosphotransfer reactions. As revealed by incubation of the GWDs with [γ-(33) P]ATP, the consumption of ATP includes the transfer of the γ-phosphate group to the GWD protein but this autophosphorylation does not require the conserved histidine residue. Thus, the GWD proteins possess two vicinal phosphorylation sites, both of which are transiently phosphorylated. Following autophosphorylation at both sites, native dikinases flexibly use various terminal phosphate acceptors, such as water, α-glucans, AMP and ADP. A model is presented describing the complex phosphotransfer reactions of GWDs as affected by the availability of the various acceptors.     

The analysis of the different functions of starch‐phosphorylating enzymes during the development of Arabidopsis thaliana plants discloses an unexpected role for the cytosolic isoform GWD2

The genome of Arabidopsis thaliana encodes three glucan, water dikinases. Glucan, water dikinase 1 (GWD1; EC 2.7.9.4) and phosphoglucan, water dikinase (PWD; EC 2.7.9.5) are chloroplastic enzymes, while glucan, water dikinase 2 (GWD2) is cytosolic. Both GWDs and PWD catalyze the addition of phosphate groups to amylopectin chains at the surface of starch granules, changing its physicochemical properties. As a result, GWD1 and PWD have a positive effect on transitory starch degradation at night. Because of its cytosolic localization, GWD2 does not have the same effect. Single T‐DNA mutants of either GWD1 or PWD or GWD2 have been analyzed during the entire life cycle of A. thaliana. We report that the three dikinases are all important for proper seed development. Seeds from gwd2 mutants are shrunken, with the epidermal cells of the seed coat irregularly shaped. Moreover, gwd2 seeds contain a lower lipid to protein ratio and are impaired in germination. Similar seed phenotypes were observed in pwd and gwd1 mutants, except for the normal morphology of epidermal cells in gwd1 seed coats. The gwd1, pwd and gwd2 mutants were also very similar in growth and flowering time when grown under continuous light and all three behaved differently from wild‐type plants. Besides pinpointing a novel role of GWD2 and PWD in seed development, this analysis suggests that the phenotypic features of the dikinase mutants in A. thaliana cannot be explained solely in terms of defects in leaf starch degradation at night.     

Phosphorylation of C6- and C3-positions of glucosyl residues in starch is catalysed by distinct dikinases

Glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD) are required for normal starch metabolism. We analysed starch phosphorylation in Arabidopsis wild-type plants and mutants lacking either GWD or PWD using (31)P NMR. Phosphorylation at both C6- and C3-positions of glucose moieties in starch was drastically decreased in GWD-deficient mutants. In starch from PWD-deficient plants C3-bound phosphate was reduced to levels close to the detection limit. The latter result contrasts with previous reports according to which GWD phosphorylates both C6- and C3-positions. In these studies, phosphorylation had been analysed by HPLC of acid-hydrolysed glucans. We now show that maltose-6-phosphate, a product of incomplete starch hydrolysis, co-eluted with glucose-3-phosphate under the chromatographic conditions applied. Re-examination of the specificity of the dikinases using an improved method demonstrates that C6- and C3-phosphorylation is selectively catalysed by GWD and PWD, respectively.     

Light-induced degradation of storage starch in turions of Spirodela polyrhiza depends on nitrate

Light induces both the germination of turions of the duckweed Spirodela polyrhiza and the degradation of the reserve starch stored in the turions. The germination photoresponse requires nitrate, and we show here that nitrate is also needed for the light-induced degradation of the turion starch. Ammonium cannot substitute for nitrate in this regard, and nitrate thus acts specifically as signal to promote starch degradation in the turions. Irradiation with continuous red light leads to starch degradation via auto-phosphorylation of starch-associated glucan, water dikinase (GWD), phosphorylation of the turion starch and enhanced binding of alpha-amylase to starch granules. The present study shows that all of these processes require the presence of nitrate, and that nitrate exerts its effect on starch degradation at a point between the absorption of light by phytochrome and the auto-phosphorylation of the GWD. Nitrate acts to coordinate carbon and nitrogen metabolism in germinating turions: starch will only be broken down when sufficient nitrogen is present to ensure appropriate utilization of the released carbohydrate. These data constitute the first report of control over the initiation of reserve starch degradation by nitrate.     

The Two Plastidial Starch-Related Dikinases Sequentially Phosphorylate Glucosyl Residues at the Surface of Both the A- and B-Type Allomorphs of Crystallized Maltodextrins But the Mode of Action Differs

In this study, two crystallized maltodextrins were generated that consist of the same oligoglucan pattern but differ strikingly in the physical order of double helices. As revealed by x-ray diffraction, they represent the highly ordered A- and B-type allomorphs. Both crystallized maltodextrins were similar in size distribution and birefringence. They were used as model substrates to study the consecutive action of the two starch-related dikinases, the glucan, water dikinase and the phosphoglucan, water dikinase. The glucan, water dikinase and the phosphoglucan, water dikinase selectively esterify glucosyl residues in the C6 and C3 positions, respectively. Recombinant glucan, water dikinase phosphorylated both allomorphs with similar rates and caused complete glucan solubilization. Soluble neutral maltodextrins inhibited the glucan, water dikinase-mediated phosphorylation of crystalline particles. Recombinant phosphoglucan, water dikinase phosphorylated both the A- and B-type allomorphs only following a prephosphorylation by the glucan, water dikinase, and the activity increased with the extent of prephosphorylation. The action of the phosphoglucan, water dikinase on the prephosphorylated A- and B-type allomorphs differed. When acting on the B-type allomorph, by far more phosphoglucans were solubilized as compared with the A type. However, with both allomorphs, the phosphoglucan, water dikinase formed significant amounts of monophosphorylated phosphoglucans. Thus, the enzyme is capable of acting on neutral maltodextrins. It is concluded that the actual carbohydrate substrate of the phosphoglucan, water dikinase is defined by physical rather than by chemical parameters. A model is proposed that explains, at the molecular level, the consecutive action of the two starch-related dikinases.In terms of quantity, starch is one of the most prominent photosynthesis-derived products. The global starch production by land plants has been estimated to be approximately 2,850 million tons per year (Burrell, 2003). Starch is highly relevant for nutrition in animals and humans, but it is also used for many industrial applications, such as additives in paper or textiles and in pharmacy products as well. In addition, starch appears to be increasingly important as a photosynthesis-based renewable energy source that can be converted into technologically relevant products such as bioethanol and hydrogen (Hannah and James, 2008; Zhang et al., 2008).Native starch is formed as a water-insoluble particle called a granule that is thought to comprise two types of polyglucans, amylopectin and amylose. The latter is an almost unbranched α-1,4-glucan and usually is the minor constituent of the starch particle, accounting for 10% to 35% of the total starch dry weight (Ball, 2000). However, in some mutants, the relative amylose content is strongly diminished, resulting in an essentially amylose-free starch (such as in the waxy mutant of maize [Zea mays]), or, alternatively, it is increased, forming up to 70% of the starch mass (e.g. in the amylose extender mutant from maize; Gérard et al., 2001). Nevertheless, in wild-type starches, amylopectin typically is the major constituent that also is essential for the molecular organization of the glucans within the entire starch granule (Ball and Morell, 2003). Like glycogen, amylopectin is a branched α-glucan with 4% to 6% of the inter-Glc linkages being α-1,6-bonds (Ball, 2000); however, as opposed to glycogen, the branching points occur as intramolecular clusters. Due to the length distribution of the side chains and the clustering of the branching points, neighboring glucan chains are capable of forming highly ordered double helices (Smith, 2001; Zeeman et al., 2002).As revealed by x-ray diffraction analysis, two major native starch structures are known that differ in the arrangement of the double helices. The A-type allomorph, which is typical of wild-type cereal starches but also occurs in lower plants, is more compact, as compared with the B type, and consists of flat layers of double helices. By contrast, in the B-type allomorph, six double helices are thought to surround a central cavity that is filled with water molecules. The B-type allomorph is found in starch synthesized by dicotyledonal storage organs, such as potato (Solanum tuberosum) tubers, in some high-amylose starches from cereal mutants (Gallant et al., 1997; Gérard et al., 2001), and in assimilatory starches from potato and Arabidopsis (Arabidopsis thaliana) as well (Hejazi et al., 2008). Legume starches are believed to represent another allomorph that is designated the C type. However, this allomorph is actually a mixture of both the A- and B-type crystallites within a single native starch particle rather than a third distinct type of the double helical arrangement (Imberty et al., 1991; Bogracheva et al., 2001).It should be noted that both the A- and B-type allomorphs of native starch granules often contain, as a minor constituent, an additional crystal structure designated the V type. Unlike the A- and B-type allomorphs, the V type is assumed to arise from single amylose helices, some of which are complexed with endogenous granular lipids. When estimated for the dry state, the V-type crystal structure accounts for only a small percentage of the total starch granule crystallinity (Lopez-Rubio et al., 2008).The physical structure of the native starch particle is likely to have important biochemical implications, as it affects the performance of carbohydrate-active enzymes and, thereby, the transition of carbohydrates from the solid phase to the soluble phase. This conclusion has been reached by in vitro experiments demonstrating that the pancreas α-amylase hydrolyzes A-type starch faster than the B-type counterpart (Gérard et al., 2001).Another metabolically important feature of amylopectin is the occurrence of covalent modification by phosphate esters that are found in a small proportion of the glucosyl residues. Most frequently phosphorylation occurs at the C6 position of the glucosyl residue, but C3 and, to a minor extent, C2 can also be esterified (Hizukuri et al., 1970). Recently, evidence has been presented that the esterification of the C6 and C3 positions of glucosyl residues differs in the structural effects on the neighboring inter-Glc bonds (Hansen et al., 2009). Phosphorylation at C6 is mediated by the recently identified α-glucan, water dikinase (GWD; EC 2.7.9.4), which utilizes ATP as dual phosphate donor and three distinct acceptors, two of which are sequentially used. The enzyme transfers the terminal phosphate group to water (thereby forming orthophosphate) and the β-phosphate group first to a conserved His residue within the catalytic domain of the monomeric GWD and, subsequently, to the C6 target of the glucosyl residue to be phosphorylated (Ritte et al., 2002, 2006). Phosphorylation at C3 is catalyzed by a second dikinase, designated phosphoglucan, water dikinase (PWD; EC 2.7.9.5; Ritte et al., 2006). The amino acid sequence of the catalytic (C-terminal) domain of PWD shares similarity with that of GWD, and in principle, the PWD-mediated catalysis follows the same mode of action as GWD, including the transient autophosphorylation at a conserved His residue (Baunsgaard et al., 2005; Kötting et al., 2005). However, PWD deviates from GWD in the amino acid sequence of the N-terminal domain, especially in the carbohydrate-binding region. PWD possesses a single carbohydrate-binding module that has been grouped into the family CBM20 (Machovič and Janaček, 2006a, 2006b). By contrast, the N-terminal domain of GWD contains two putative carbohydrate-binding motifs similar to those of an α-amylase that presumably is located in the chloroplasts (Yu et al., 2005). However, the structure of these motifs is still not known; therefore, a sequence-based prediction of the actual carbohydrate target is not yet possible.GWD- and PWD-deficient Arabidopsis mutants possess to some extent similar but not equal phenotypes. Leaves of GWD-deficient lines (which contain essentially unchanged levels of functional PWD) have starch levels that are at least five times higher than those of the wild type and remain high even after prolonged darkness. Growth of the entire plant is strongly compromised. The phenotype of PWD-deficient mutants (which express functional GWD) is less severe, as growth is only slightly diminished and transitory starch levels are elevated but not as strongly as in the GWD-deficient lines. Mutants lacking functional PWD can degrade transitory starch, but net degradation occurs at a lower rate as compared with wild-type plants (Kötting et al., 2005). These data clearly indicate that, in vivo, PWD cannot substitute for GWD and that glucosyl 6-phosphate residues are involved in a more strict control of the starch turnover as compared with the C3 phosphate esters.When considering the metabolic function(s) of starch phosphorylation, it should be noted that phosphorylation occurs during both net starch synthesis and degradation, although the rates of phosphorylation are likely to be different (Nielsen et al., 1994; Ritte et al., 2004). It is reasonable, therefore, to assume that starch phosphorylation exerts an important role in the entire transitory starch metabolism, rather than being functional only during the degrading process (and, consequently, the starch-related dikinases cannot, in a strict sense, be considered as “starch-degrading enzymes”).Depending on the botanical source, the degree of starch phosphorylation varies strongly. In potato tuber starch, approximately 0.1% to 0.5% of the glucosyl residues are phosphorylated (Ritte et al., 2002), and this value is considered to be indicative of a high level of phosphorylation. By contrast, cereal starches contain a far lower relative phosphate content that often is close to the limit of detection (approximately 0.002%; Glaring et al., 2006). In principle, these differences could be due to different rates of phosphorylation, as catalyzed by the two starch-related dikinases, and this assumption seems to be supported by the observation that, in general, starches of the B-type allomorph appear to have a higher degree of phosphorylation as compared with those of the A-type allomorph. If so, the dikinases may preferentially act on the B-type allomorph. Alternatively, the phosphorylation catalyzed by the two dikinases could be balanced by counteracting phosphatases, such as SEX4. This plastidial enzyme has been shown to act as a (phospho)glucan phosphatase that is involved in leaf starch metabolism (Kötting et al., 2009). If antagonistic enzyme activities are taken into consideration, the actual level of starch phosphorylation is determined by the rate of both phosphorylation and the subsequent hydrolysis of phosphate esters and, consequently, does not necessarily reflect the action of the starch-related dikinases.Recently, crystallized maltodextrins (MD_cryst) have been prepared that, by using x-ray diffraction, were identified as being the B-type allomorph and to possess a highly ordered structure (which exceeds that of native starch granules). MD_cryst have been applied as a substrate for a recombinant GWD from potato. Using a carefully optimized assay, the rate of phosphorylation was by far higher than that observed with any other carbohydrate substrate, such as native starch granules or starch-derived polysaccharides. By contrast, solubilization by heat treatment of the MD_cryst almost completely abolished the activity of GWD. Phosphorylation resulted in the formation of singly, doubly, and triply phosphorylated glucans and favored the solubilization of both neutral glucans and phosphoglucans (Hejazi et al., 2008). Recombinant PWD also phosphorylated MD_cryst, provided the MD_cryst had been prephosphorylated by GWD and were not solubilized by heat treatment (Hejazi et al., 2008).Because of the high phosphorylation rates and the phosphorylation pattern obtained, MD_cryst are a suitable model carbohydrate that mimics phosphorylation-relevant features of highly ordered regions within the native starch granule. It allows study of the action of the two starch-related dikinases and the transition of carbohydrates from the solid to the soluble state without any other starch-related enzyme being required.Until now, only the B-type allomorph of the MD_cryst has been applied as substrate of the two dikinases. Using native starch granules as a target, the rates of phosphorylation as obtained with recombinant GWD varied largely within the B-type allomorph (Hejazi et al., 2008); therefore, it is reasonable to assume that additional but largely unknown features of the native starch granule also strongly affect the action of GWD. This implies that any preference or specificity of the starch-related dikinases for a given allomorph can be analyzed most convincingly if MD_cryst preparations representing both the B- and A-type allomorphs are available.In this study, we used two MD_cryst preparations that are indistinguishable in their oligoglucan patterns but differ in the physical arrangement of the double helices and represent the highly ordered A- and B-type allomorphs. Using these two MD_cryst preparations, we analyzed the action of the two starch-related dikinases. The size distribution of the MD_cryst particles has been determined using the Coulter counter, and surface properties of both allomorphs were monitored by scanning electron microscopy. Thermal stability of the two allomorphs was analyzed by measuring the temperature dependence of light scattering. Finally, the phosphorylation-dependent solubilization of both allomorphs and the transition of (phospho)glucans into the soluble state have been studied.     

Dynamics of starch granule biogenesis – the role of redox-regulated enzymes and low-affinity carbohydrate-binding modules

Abstract

The deposition and degradation of starch in plants is subject to extensive post-translational regulation. To permit degradation of B-type crystallites present in tuberous and leaf starch these starch types are phosphorylated by glucan, water dikinase (GWD). At the level of post-translational redox regulation, ADPglucose pyrophosphorylase, β-amylase (BAM1), limit dextrinase (LD), the starch phosphorylator GWD and the glucan phosphatase dual-specificity phosphatase 4 (DSP4), also named starch excess 4 (SEX4), are reductively activated in vitro. Redox screens now suggest the presence of a substantially more extensive and coordinated redox regulation involving a larger number of enzymes. Noticeably several of these enzymes contain a new type of low-affinity carbohydrate-binding module that we term a low-affinity starch-binding domain or LA-SBD. These are present in the CBM20, CBM45 and CBM53 families and can enable diurnal dynamics of starch–enzyme recognition. Such diurnal changes in starch binding have been indicated for the redox-regulated GWD and SEX4.     

A CBM20 low-affinity starch-binding domain from glucan, water dikinase

The family 20 carbohydrate-binding module (CBM20) of the Arabidopsis starch phosphorylator glucan, water dikinase 3 (GWD3) was heterologously produced and its properties were compared to the CBM20 from a fungal glucoamylase (GA). The GWD3 CBM20 has 50-fold lower affinity for cyclodextrins than that from GA. Homology modelling identified possible structural elements responsible for this weak binding of the intracellular CBM20. Differential binding of fluorescein-labelled GWD3 and GA modules to starch granules in vitro was demonstrated by confocal laser scanning microscopy and yellow fluorescent protein-tagged GWD3 CBM20 expressed in tobacco confirmed binding to starch granules in planta.     

In-vitro degradation of starch granules isolated from spinach chloroplasts

The initial reactions of transitory starch degradation in Spinacia oleracea L. were investigated using an in-vitro system composed of native chloroplast starch granules, purified chloroplast and non-chloroplast forms of phosphorylase (EC 2.4.1.1) from spinach leaves, and -amylase (EC 3.2.1.1) isolated from Bacillus subtilis. Starch degradation was followed by measuring the release of soluble glucans, by determining phosphorylase activity, and by an electron-microscopic evaluation following deep-etching of the starch granules. Starch granules were readily degraded by -amylase but were not a substrate for the chloroplast phosphorylase. Phosphorolysis and glucan synthesis by this enzyme form were strictly dependent upon a preceding amylolytic attack on the starch granules. In contrast, the non-chloroplast phosphorylase was capable of using starch-granule preparations as substrate. Hydrolytic degradation of the starch granules was initiated at the entire particle surface, independently of its size. As a result of amylolysis, soluble glucans were released with a low degree of polymerization. When assayed with these glucans as substrate, the chloroplast phosphorylase form exhibited a higher apparent affinity and a higher reaction velocity compared with the non-chloroplast phosphorylase form. It is proposed that transitory starch degradation in vivo is initiated by hydrolysis; phosphorolysis is most likely restricted to a pool of soluble glucan intermediates.Abbreviations Glc1P Glucose 1-phosphate - Mes 2(N-morpholino)ethanesulfonic acid - Pi Orthophosphate     

A novel isoform of glucan, water dikinase phosphorylates pre-phosphorylated alpha-glucans and is involved in starch degradation in Arabidopsis

An Arabidopsis thaliana gene encoding a homologue of the potato alpha-glucan, water dikinase GWD, previously known as R1, was identified by screening the Arabidopsis genome and named AtGWD3. The AtGWD3 cDNA was isolated, heterologously expressed and the protein was purified to apparent homogeneity to determine the enzymatic function. In contrast to the potato GWD protein, the AtGWD3 primarily catalysed phosphorylation at the C-3 position of the glucose unit of preferably pre-phosphorylated amylopectin substrate with long side chains. An Arabidopsis mutant, termed Atgwd3, with downregulated expression of the AtGWD3 gene was analysed. In Atgwd3 the amount of leaf starch was constantly higher than wild type during the diurnal cycle. Compared with wild-type leaf starch, the level of C-3 phosphorylation of the glucosyl moiety of starch in this mutant was reduced. Taken together, these data indicate that the C-3 linked phospho-ester in starch plays a so far unnoticed specific role in the degradation of transitory starch.     

The legwd mutant uncovers the role of starch phosphorylation in pollen development and germination in tomato

Starches extracted from most plant species are phosphorylated. α-Glucan water dikinase (GWD) is a key enzyme that controls the phosphate content of starch. In the absence of its activity starch degradation is impaired, leading to a starch excess phenotype in Arabidopsis and in potato leaves, and to reduced cold sweetening in potato tubers. Here, we characterized a transposon insertion ( legwd::Ds ) in the tomato GWD ( LeGWD ) gene that caused male gametophytic lethality. The mutant pollen had a starch excess phenotype that was associated with a reduction in pollen germination. SEM and TEM analyses indicated mild shrinking of the pollen grains and the accumulation of large starch granules inside the plastids. The level of soluble sugars was reduced by 1.8-fold in mutant pollen grains. Overall, the transmission of the mutant allele was only 0.4% in the male, whereas it was normal in the female. Additional mutant alleles, obtained through transposon excision, showed the same phenotypes as legwd::Ds . Moreover, pollen germination could be restored, and the starch excess phenotype could be abolished in lines expressing the potato GWD homolog ( StGWD ) under a pollen-specific promoter. In these lines, where fertility was restored, homozygous plants for legwd::Ds were isolated, and showed the starch excess phenotype in the leaves. Overall, our results demonstrate the importance of starch phosphorylation and breakdown for pollen germination, and open up the prospect for analyzing the role of starch metabolism in leaves and fruits.     

Glucan, water dikinase activity stimulates breakdown of starch granules by plastidial beta-amylases

Glucan phosphorylating enzymes are required for normal mobilization of starch in leaves of Arabidopsis (Arabidopsis thaliana) and potato (Solanum tuberosum), but mechanisms underlying this dependency are unknown. Using two different activity assays, we aimed to identify starch degrading enzymes from Arabidopsis, whose activity is affected by glucan phosphorylation. Breakdown of granular starch by a protein fraction purified from leaf extracts increased approximately 2-fold if the granules were simultaneously phosphorylated by recombinant potato glucan, water dikinase (GWD). Using matrix-assisted laser-desorption ionization mass spectrometry several putative starch-related enzymes were identified in this fraction, among them beta-AMYLASE1 (BAM1; At3g23920) and ISOAMYLASE3 (ISA3; At4g09020). Experiments using purified recombinant enzymes showed that BAM1 activity with granules similarly increased under conditions of simultaneous starch phosphorylation. Purified recombinant potato ISA3 (StISA3) did not attack the granular starch significantly with or without glucan phosphorylation. However, starch breakdown by a mixture of BAM1 and StISA3 was 2 times higher than that by BAM1 alone and was further enhanced in the presence of GWD and ATP. Similar to BAM1, maltose release from granular starch by purified recombinant BAM3 (At4g17090), another plastid-localized beta-amylase isoform, increased 2- to 3-fold if the granules were simultaneously phosphorylated by GWD. BAM activity in turn strongly stimulated the GWD-catalyzed phosphorylation. The interdependence between the activities of GWD and BAMs offers an explanation for the severe starch excess phenotype of GWD-deficient mutants.     

The binding of α-amylase to starch plays a decisive role in the initiation of storage starch degradation in turions of Spirodela polyrhiza

Degradation of reserve starch in turions, perennation organs of the duckweed Spirodela polyrhiza , is induced by continuous red light (cR). Irradiation of the turions with this light results in the autophosphorylation of starch-associated glucan water dikinase (GWD). The ensuing phosphorylation of the starch by this enzyme was proposed to result in the enhanced association of starch-degrading enzymes to the starch granules and in the initiation of starch breakdown. The present results confirm that the irradiation of dark-adapted turions with cR results in phosphorylation of the starch, accompanying changes in the capacity of the granule starch to bind turion endogenous α-amylase, as well as changes in the starch degradation level. All three effects show very similar dependence on the time of irradiation, suggesting that they may be linked. The α-amylase is a plausible candidate for effecting starch breakdown initiation. However, the increased binding capacity of the starch granules for this enzyme is insufficient to account for the initiation of the starch breakdown as this capacity is already high prior to the irradiation. The decisive effect of cR irradiation on starch degradation may lie in enabling α-amylase to gain access to otherwise sequestered starch granules or in activating α-amylase bound to the granules.     

Light induces phosphorylation of glucan water dikinase, which precedes starch degradation in turions of the duckweed Spirodela polyrhiza

Degradation of storage starch in turions, survival organs of Spirodela polyrhiza, is induced by light. Starch granules isolated from irradiated (24 h red light) or dark-stored turions were used as an in vitro test system to study initial events of starch degradation. The starch-associated pool of glucan water dikinase (GWD) was investigated by two-dimensional gel electrophoresis and by western blotting using antibodies raised against GWD. Application of this technique allowed us to detect spots of GWD, which are light induced and absent on immunoblots prepared from dark-adapted plants. These spots, showing increased signal intensity following incubation of the starch granules with ATP, became labeled by randomized [betagamma-33P]ATP but not by [gamma-33P]ATP and were removed by acid phosphatase treatment. This strongly suggests that they represent a phosphorylated form(s) of GWD. The same light signal that induces starch degradation was thus demonstrated for the first time to induce autophosphorylation of starch-associated GWD. The in vitro assay system has been used to study further effects of the light signal that induces autophosphorylation of GWD and starch degradation. In comparison with starch granules from dark-adapted plants, those from irradiated plants showed increase in (1) binding capacity of GWD by ATP treatment decreased after phosphatase treatment; (2) incorporation of the beta-phosphate group of ATP into starch granules; and (3) rate of degradation of isolated granules by starch-associated proteins, further enhanced by phosphorylation of starch. The presented results provide evidence that autophosphorylation of GWD precedes the initiation of starch degradation under physiological conditions.     

Structural and thermodynamic properties of starches extracted from GBSS and GWD suppressed potato lines

A combined DSC–SAXS approach was employed to study the effects of amylose and phosphate esters on the assembly structures of amylopectin in B-type polymorphic potato tuber starches. Amylose and phosphate levels in the starches were specifically engineered by antisense suppression of the granule bound starch synthase (GBSS) and the glucan water dikinase (GWD), respectively. Joint analysis of the SAXS and DSC data for the engineered starches revealed that the sizes of amylopectin clusters, thickness of crystalline lamellae and the polymorphous structure type remained unchanged. However, differences were found in the structural organization of amylopectin clusters reflected in localization of amylose within these supramolecular structures. Additionally, data for annealed starches shows that investigated potato starches possess different types of amylopectin defects. The relationship between structure of investigated potato starches and their thermodynamic properties was recognized.     

A novel type carbohydrate-binding module identified in alpha-glucan, water dikinases is specific for regulated plastidial starch metabolism

The phosphorylation of the amylopectin fraction of starch catalyzed by the alpha-glucan, water dikinase (GWD, EC 2.7.9.4) plays a pivotal role in starch metabolism. Limited proteolysis of the potato tuber (Solanum tuberosum) GWD (StGWD, 155 kDa) by trypsin primarily produced stable fragments of 33 and 122 kDa, termed the SBD fragment and N11, respectively, as generated by trypsin cleavage at Arg-286. SBD and N11 were generated using recombinant DNA technology and purified to near homogeneity. Tandem repeat sequences, SBD-1 and SBD-2, of a region that is significantly similar in sequence to N-terminal regions of plastidial alpha-amylases are located in the N-terminus of StGWD. The SBD-1 motif is located within the sequence of the SBD fragment, and our results demonstrate that the fragment composes a new and novel carbohydrate-binding module (CBM), apparently specific for plastidial alpha-glucan degradation. By mutational analyses of conserved Trp residues located within the SBD-1 motif, W62 and W117, we show that these aromatic residues are vital for carbohydrate binding. N11 still possessed starch phosphorylating activity, but with a 2-fold higher specific activity compared to that of wild type (WT) StGWD using potato starch as the glucan substrate, whereas it had double the K(m) value for the same substrate. Furthermore, investigation of the chains phosphorylated by WT StGWD and N11 shows that N11 exhibits a higher preference for phosphorylating shorter chains of the amylopectin molecule as compared to WT. From analyses of the glucan substrate specificity, we found up to 5-fold higher specific activity for N11 using amylose as the substrate.