Antisense inhibition of plastidial phosphoglucomutase provides compelling evidence that potato tuber amyloplasts import carbon from the cytosol in the form of glucose-6-phosphate

The aim of this work was to establish whether plastidial phosphoglucomutase is involved in the starch biosynthetic pathway of potato tubers and thereby to determine the form in which carbon is imported into the potato amyloplast. For this purpose, we cloned the plastidial isoform of potato PGM (StpPGM), and using an antisense approach generated transgenic potato plants that exhibited decreased expression of the StpPGM gene and contained significantly reduced total phosphoglucomutase activity. We confirmed that this loss in activity was due specifically to a reduction in plastidial PGM activity. Potato lines with decreased activities of plastidial PGM exhibited no major changes in either whole-plant or tuber morphology. However, tubers from these lines exhibited a dramatic (up to 40%) decrease in the accumulation of starch, and significant increases in the levels of sucrose and hexose phosphates. As tubers from these lines exhibited no changes in the maximal catalytic activities of other key enzymes of carbohydrate metabolism, we conclude that plastidial PGM forms part of the starch biosynthetic pathway of the potato tuber, and that glucose-6-phosphate is the major precursor taken up by amyloplasts in order to support starch synthesis.     

Starch synthesis in amyloplasts purified from developing potato tubers

Amyloplasts have been purified from potato tubers by mechanical homogenization and gravity sedimentation through Nycodenz. Based on the recovery and latency of organelle-specific marker enzymes, the recovery of amyloplasts is approximately 13%, exhibiting 65% intactness, with less than 1% contamination by other subcellular fractions. These preparations were able to synthesize starch from glucose-1-phosphate plus ATP, or ADP-glucose but not from glucose-6-phosphate. Rates of starch synthesis from glucose-1-phosphate plus ATP were linear for up to 1 h and sensitive to the inhibitor 4,4-diisothiocyanato-stilbene 2,2-disulphonic acid (DIDS). Starch synthesis was optimal at pH 7.0 and was saturated by 5–10 mM glucose-1-phosphate and by 1 mM ADP-glucose. The results are discussed in the context of the pathway of starch synthesis and the transport of metabolites across the amyloplast envelope.     

Starch synthesis in transgenic potato tubers with increased 3-phosphoglyceric acid content as a consequence of increased 6-phosphofructokinase activity

The aim of this work was to test the hypothesis that changes in cytosolic 3-phosphoglyceric acid (3-PGA) content can regulate the rate of starch synthesis in potato (Solanum tuberosum L.) tubers. The amount of 3-PGA was increased by expressing bacterial phosphofructokinase (PFK; EC 2.7.1.11) in transgenic potato tubers. The resultant 3-fold increase in PFK activity was accompanied by an increase in metabolites downstream of PFK, including a 3-fold increase in 3-PGA. There was also a decrease in metabolites upstream of PFK, most notably of glucose-6-phosphate. The increase in 3-PGA did not affect the amount of starch that accumulated in developing tubers, nor its rate of synthesis in tuber discs cut from developing tubers. This suggests that changes in cytosolic 3-PGA may not affect the rate of starch synthesis under all circumstances. We propose that in this case, a decrease in glucose-6-phosphate (which is transported into the amyloplast as a substrate for starch synthesis) may be sufficient to counteract the effect of increased 3-PGA.     

Mechanism of starch-sugar interconversion in Solanum tuberosum

The changes in glucose-1-phosphate, glucose-6-phosphate, fructose-6-phosphate, dihydroxyacetone phosphate, 3-phosphoglycerate, 2-phospho-glycerate, phosphoenol-pyruvate, pyruvate, adenosine mono-, di- and tri-phosphates, NAD and NADH, sugars and respiration of mature potato tubers (variety King Edward) caused by transfer from + 10° to + 2° and back to + 10° were followed throughout 4–8 weeks of storage. The results obtained showed a characteristic two phase pattern. In the case of the transfer from + 10° to + 2° a number of the phosphate esters showed wide individual variations in concentration during the first phase but only slow changes during the second phase when most of the phosphate esters tended to follow a common pattern. In the first phase the sugar concentration remained roughly constant, but in the second a considerable increase in both sucrose and respiration occurred. In the case of potatoes transferred from + 2° to + 10° the two phase character of the results was not so marked. In the case of potatoes transferred from + 10° to + 2° the changes in the phosphate esters in the first phase did not appear to be related to the conversion of starch to sucrose which only occurred to a significant extent in the second phase. Electron micrographs of potato tubers which had been stored at + 2° for 38 days (sugar content 2.4%) showed that the starch grains were still enclosed in a double membrane (amyloplast membrane). Analysis of starch grains prepared by a non-aqueous method from potato tubers stored at + 10° and + 2° indicated that a large part of the K, Na, Cl, citrate and glucose-6-phosphate was inside the amyloplast but that the sugar (storage at + 2°) was outside; sweetening therefore involved the transport of metabolites through the amyloplast membrane. Comparison with other treatments (anaerobiosis, cyanide, ethylene chlorhydrin) which cause sweetening suggested that the regulation of the starch-sugar interconversion was effected at the amyloplast membrane and possibly involved electron transfer. In the case of potatoes which sweetened due to senescence, electron micrographs showed that the amyloplast membranes were disintegrating.     

Effect of chlorocholine chloride sprays on the carbohydrate composition and activities of sucrose metabolising enzymes in potato (Solanum tuberosum L.)

Chlorocholine chloride (CCC) was sprayed on a potato crop 25 days after sowing (DAS) at 5 day intervals for a total of 7 sprays. Activity of sucrose synthase (SS) in the sucrose cleavage direction was many fold higher than that of acid invertase in all the tissues. The activity of alkaline invertase was negligible. A sharp decline in the starch content of stolons of the CCC-sprayed crop was observed between 60 DAS and 70 DAS. This could divert the carbon towards tubers and thus enhancing its availability for starch synthesis. The CCC-treated crop, in general, had higher SS (cleavage) activity in stem, stolons and tubers. A higher sucrose content in the stem of the CCC-treated crop could be due to the high sucrose phosphate synthase (SPS) activity observed in this plant part. In tubers of CCC-treated crops a higher SS (cleavage) activity along with a high sucrose content in tubers during the active tuber filling stage could lead to better availability of UDP-glucose for its conversion to glucose-1-phosphate, which could enter into the amyloplast leading to higher starch content. High SPS activity in tubers of CCC-treated plants ensures that reducing sugars formed are reconverted efficiently to sucrose. The efficiency of developing tubers from CCC-sprayed plants to convert 14C sucrose fed through stolons into starch was about 2.5 times more than in the control.     

Effect of temperature on starch synthesis in potato tuber tissue and in amyloplasts

A sharp temperature optimum is observed at 21.5°C when the incorporation of [¹⁴C]sucrose into starch is measured with discs cut from developing tubers of potato (Solanum tuberosum L. cv Desirée). By contrast, increasing temperatures over the range 9 to 31°C only enhance release of ¹⁴C to respiratory CO₂ and incorporation of ¹⁴C into the ethanolsoluble fraction. By comparison, starch synthesis in discs from developing corms of cocoyam (Colocasia esculenta L. Schott) is increased by raising the temperature from 15 to 35°C. The significance of a relatively low temperature optimum for starch synthesis in potato is discussed in relation to the yield limitations imposed by continuously high soil temperatures. Amyloplasts isolated from protoplasts prepared from developing potato tubers contain activities of alkaline pyrophosphatase, NAD-dependent glyceraldehyde-3-phosphate dehydrogenase, fructose-1,6-bisphosphatase, and phosphoglucomutase in addition to ADP-glucose-pyrophosphorylase, starch phosphorylase and starch synthase. Cell-free amyloplasts released by thinly slicing developing potato tubers synthesize starch from [¹⁴C]triose-phosphate generated from [¹⁴C]fructose-1,6-bisphosphate in the reaction medium. This starch synthesis is inhibited by addition of 10 millimolar inorganic phosphate and requires amyloplast integrity, suggesting the operation of a triose-phosphate/inorganic phosphate exchange carrier at the amyloplast membrane. The temperature optimum at 21.5°C observed with tissue discs is not observed with amyloplasts.     

Starch biosynthesis from triose-phosphate in transgenic potato tubers expressing plastidic fructose-1,6-bisphosphatase

A full length cDNA clone encoding plastidic fructose-1,6-bisphosphatase (cp-FBPase), together with a transit peptide, was isolated from a potato (Solanum tuberosum L.) leaf cDNA library. Potato plants were transformed with the isolated cp-FBPase sequence behind a patatin class I promoter to ensure tuber-specific expression of the enzyme. Plant lines were selected which expressed up to 250 mU (g FW)-1 in the developing tubers, which is 10- to 20-fold the activity found in wild-type tubers. Intact amyloplasts were isolated from in vitro-grown minitubers developed in darkness. Comparison with marker enzymes showed that cp-FBPase activity in transgenic tubers, as well as the low FBPase activity in the wild-type tubers, was localised inside the amyloplasts. The intact amyloplasts isolated from both wild-type and transgenic tubers synthesised starch from [U-14C] glucose-6-phosphate. Conversely, only the transgenic tubers expressing cp-FBPase showed appreciable synthesis of starch from [U-14C] dihydroxyacetone phosphate, and this synthesis rate was correlated to the activity of cp-FBPase. Thus, the expression of cp-FBPase in tubers allows for a new route of starch biosynthesis from triose-phosphates imported from the cytosol. The transgenic tubers did not differ from wild-type tubers with respect to starch content, or the levels of neutral sugars and phosphorylated hexoses.     

The three-dimensional distribution of minerals in potato tubers

Background and Aims

The three-dimensional distributions of mineral elements in potato tubers provide insight into their mechanisms of transport and deposition. Many of these minerals are essential to a healthy human diet, and characterizing their distribution within the potato tuber will guide the effective utilization of this staple foodstuff.

Methods

The variation in mineral composition within the tuber was determined in three dimensions, after determining the orientation of the harvested tuber in the soil. The freeze-dried tuber samples were analysed for minerals using inductively coupled plasma-mass spectrometry (ICP-MS). Minerals measured included those of nutritional significance to the plant and to human consumers, such as iron, zinc, copper, calcium, magnesium, manganese, phosphorus, potassium and sulphur.

Key Results

The concentrations of most minerals were higher in the skin than in the flesh of tubers. The potato skin contained about 17 % of total tuber zinc, 34 % of calcium and 55 % of iron. On a fresh weight basis, most minerals were higher in tuber flesh at the stem end than the bud end of the tuber. Potassium, however, displayed a gradient in the opposite direction. The concentrations of phosphorus, copper and calcium decreased from the periphery towards the centre of the tuber.

Conclusions

The distribution of minerals varies greatly within the potato tuber. Low concentrations of some minerals relative to those in leaves may be due to their low mobility in phloem, whereas high concentrations in the skin may reflect direct uptake from the soil across the periderm. In tuber flesh, different minerals show distinct patterns of distribution in the tuber, several being consistent with phloem unloading in the tuber and limited onward movement. These findings have implications both for understanding directed transport of minerals in plants to stem-derived storage organs and for the dietary implications of different food preparation methods for potato tubers.     

Overriding the co-limiting import of carbon and energy into tuber amyloplasts increases the starch content and yield of transgenic potato plants

Transgenic potato (Solanum tuberosum) plants simultaneously over-expressing a pea (Pisum sativum) glucose-6-phosphate/phosphate translocator (GPT) and an Arabidopsis thaliana adenylate translocator (NTT1) in tubers were generated. Double transformants exhibited an enhanced tuber yield of up to 19%, concomitant with an additional increased starch content of up to 28%, compared with control plants. The total starch content produced in tubers per plant was calculated to be increased by up to 44% in double transformants relative to the wild-type. Single over-expression of either gene had no effect on tuber starch content or tuber yield, suggesting that starch formation within amyloplasts is co-limited by the import of energy and the supply of carbon skeletons. As total adenosine diphosphate-glucose pyrophosphorylase and starch synthase activities remained unchanged in double transformants relative to the wild-type, they cannot account for the increased starch content found in tubers of double transformants. Rather, an optimized supply of amyloplasts with adenosine triphosphate and glucose-6-phosphate seems to favour increased starch synthesis, resulting in plants with increased starch content and yield of tubers.     

The amyloplast proteome of potato tuber

Potato (Solanum tuberosum) is the fourth largest crop worldwide in yield, and cv. Kuras is the major starch potato of northern Europe. Storage starch is packed densely in tuber amyloplasts, which become starch granules. Amyloplasts of soil-grown mini-tubers and agar-grown micro-tubers of cv. Kuras were purified. The mini-tuber amyloplast preparation was enriched 10-20-fold and the micro-tuber amyloplast approximately fivefold over comparative total protein extracts. Proteins separated by SDS-PAGE were digested with trypsin, analysed by mass spectrometry and identified by mascot software searches against an in-house potato protein database and the NCBI non-redundant plant database. The differential growth conditions for mini- and micro-tubers gave rise to rather different protein profiles, but the major starch granule-bound proteins were identical for both and dominated by granule-bound starch synthase I, starch synthase II and alpha-glucan water dikinase. Soluble proteins were dominated by starch phosphorylase L-1, other large proteins of the classes 'starch and sucrose metabolism', 'pentose phosphate pathway', 'glycolysis', 'amino acid metabolism', and other proteins such as plastid chaperonins. The majority of the identified proteins had a predicted plastid transit peptide, supporting their presence in the amyloplast. However, several highly expressed proteins had no transit peptide, such as starch phosphorylase H, or had a predicted mitochondrial location. Intriguingly, all polyphenol oxidases, a family of enolases, one transketolase, sulfite reductase, deoxynucleoside kinase-like and dihydroxy-acid dehydrase had twin-arginine translocation motifs, and a homologue to dihydrolipoamide dehydrogenase had a Sec (secretory) motif; these motifs usually target thylakoid-like structures.     

Transport of inorganic phosphate and C3- and C6-sugar phosphates across the envelope membranes of potato tuber amyloplasts

Amyloplasts have been isolated from tubers of potato plants (Solarium tuberosum. cv. Desirée). As it is difficult to isolate amyloplasts that have a high starch content, we used transformed plants in which the content of starch was reduced. This was achieved by decreasing the activity of ADP-glucose pyrophosphorylase by antisense techniques (Müller-Röber et al., 1992, EMBO. 11, 1229–1238). In the isolated plastids the activity of glutamine-oxoglutarate-aminotransferase (glutamate synthase, EC 2.6.1.53) was dependent upon the intactness of the plastids. For the supply of redox equivalents the addition of glucose-6-phosphate (Glc6P) was required. Glucose-1-phosphate (Glc1P) did not support glutamate synthesis. Plastids were treated with Triton X-100 and the solubilized proteins reconstituted into liposomes. Transport measurements with these liposomes revealed that inorganic phosphate (Pi), dihydroxyacetone phosphate (DHAP), 3-phosphoglycerate and Glc6P are transported in a counter-exchange mode. Transport of phosphoenolpyruvate was low and Glc1P was virtually not transported in exchange for Pi. Kinetic constants were determined for the Pi/Pi and Glc6P/Pi counter exchanges. For comparison, proteins of mitochondria from potato tubers and pea leaves were reconstituted into liposomes. As expected, the Pi/Pi exchange across the mitochondrial membrane was not affected by DHAP and Glc6P. Kinetic constants of the Pi/Pi counter exchange were determined for potato tuber mitochondria.Abbreviations DHAP dihydroxyacetone phosphate - Glc1P glucose-1-phosphate - Glc6P glucose-6-phosphate - PEP Phosphoenolpyruvate - 3-PGA 3-phosphoglycerate - Pi inorganic phosphate - Tricine N-[2-hydroxy-1,1-bis(hydroxymethyl)-ethyl] glycine This work was supported by Deutsche Forschungsgemeinschaft.     

Combining winter hardiness and forage yield in white clover (Trifolium repens) cultivated in northern environments

Background and Aims

White clover (Trifolium repens) is an important component of sustainable livestock systems around the world. Its exploitation for agriculture in the northern, marginal areas is, however, currently limited by the lack of cultivars that combine persistence and high production potential. The aims are to investigate whether it is feasible to create breeding material of white clover for these areas by combining winter hardiness of northerly populations with good yielding ability of more southerly cultivars.

Methods

A total of 166 crosses of 14 different parental combinations between winter-hardy, low-yielding populations of northern origin and high-yielding commercial cultivars of more southerly origin were tested under field conditions in Iceland and Norway and the parental populations were compared in Norway. Spaced plants were transplanted into a smooth meadow grass (Poa pratensis) sward. Dry matter yield was estimated for 2 years after planting in Norway and morphological characters associated with yielding capacity were measured at both sites.

Key Results

The results showed that southerly cultivars had larger leaves and higher yielding potential than northern types but suffered more winter damage. Significant variation was found between full-sib families within the different parental combinations for all morphological characteristics measured in all three trials. However, it was difficult to detect any consistent morphological patterns between progeny groups across trial sites. No significant correlations were found between leaflet area and survival.

Conclusions

The present study has confirmed that it should be possible to simultaneously select for good winter survival and larger leaves and, hence, higher yielding ability under marginal conditions.Key words: Breeding, morphology, spaced plants, Trifolium repens, winter survival, progeny testing     

The contribution of plastidial phosphoglucomutase to the control of starch synthesis within the potato tuber

The aim of this work was to evaluate the extent to which plastidial phosphoglucomutase (PGM) activity controls starch synthesis within potato (Solanum tuberosum L. cv. Desirée) tubers. The reduction in the activity of plastidial PGM led to both a correlative reduction in starch accumulation and an increased sucrose accumulation. The control coefficient of plastidial PGM on the accumulation of starch was estimated to approximate 0.24. The fluxes of carbohydrate metabolism were measured by investigating the metabolism of [U-14C]glucose in tuber discs from wild-type and transgenic plants. In tuber discs the control coefficient of plastidial PGM over starch synthesis was estimated as 0.36, indicating that this enzyme exerts considerable control over starch synthesis within the potato tuber.     

Inorganic pyrophosphate content and metabolites in potato and tobacco plants expressing E. coli pyrophosphatase in their cytosol

Metabolite levels and carbohydrates were investigated in the leaves of tobacco (Nicotiana tabacum L.) and leaves and tubers of potato (Solanum tuberosum L.) plants which had been transformed with pyrophosphatase from Escherichia coli. In tobacco the leaves contained two- to threefold less pyrophosphate than controls and showed a large increase in UDP-glucose, relative to hexose phosphate. There was a large accumulation of sucrose, hexoses and starch, but the soluble sugars increased more than starch. Growth of the stem and roots was inhibited and starch, sucrose and hexoses accumulated. In potato, the leaves contained two- to threefold less pyrophosphate and an increased UDP-glucose/ hexose-phosphate ratio. Sucrose increased and starch decreased. The plants produced a larger number of smaller tubers which contained more sucrose and less starch. The tubers contained threefold higher UDP-glucose, threefold lower hexose-phosphates, glycerate-3-phosphate and phosphoenolpyruvate, and up to sixfold more fructose-2,6-bisphosphatase than the wild-type tubers. It is concluded that removal of pyrophosphate from the cytosol inhibits plant growth. It is discussed how these results provide evidence that sucrose mobilisation via sucrose synthase provides one key site at which pyrophosphate is needed for plant growth, but is certainly not the only site at which pyrophosphate plays a crucial role.Abbreviations Fru2,6bisP fructose-2,6-bisphosphate - Fru6P fructose 6-phosphate - FW fresh weight - Glc1P glucose-1-phosphate - Glc6P glucose-6-phosphate - PEP phosphoenolpyruvate - 3PGA glycerate-3-phosphate - PFK phosphofructokinase - PFP pyrophosphate: fructose-6-phosphate phosphotransferase - Pi inorganic phosphate - PPi inorganic pyrophosphate - UDPGlc UDP-glucose This research was supported by the Deutsche Forschungsgemein-Schaft (SFB 137) and Sandoz AG (T.J., M.H., M.S.) and by the Bundesminister für Forschung und Technologie (U.S., L.W.).     

Reduction of the Cytosolic Phosphoglucomutase in Arabidopsis Reveals Impact on Plant Growth,Seed and Root Development,and Carbohydrate Partitioning

Phosphoglucomutase (PGM) catalyses the interconversion of glucose 1-phosphate (G1P) and glucose 6-phosphate (G6P) and exists as plastidial (pPGM) and cytosolic (cPGM) isoforms. The plastidial isoform is essential for transitory starch synthesis in chloroplasts of leaves, whereas the cytosolic counterpart is essential for glucose phosphate partitioning and, therefore, for syntheses of sucrose and cell wall components. In Arabidopsis two cytosolic isoforms (PGM2 and PGM3) exist. Both PGM2 and PGM3 are redundant in function as single mutants reveal only small or no alterations compared to wild type with respect to plant primary metabolism. So far, there are no reports of Arabidopsis plants lacking the entire cPGM or total PGM activity, respectively. Therefore, amiRNA transgenic plants were generated and used for analyses of various parameters such as growth, development, and starch metabolism. The lack of the entire cPGM activity resulted in a strongly reduced growth revealed by decreased rosette fresh weight, shorter roots, and reduced seed production compared to wild type. By contrast content of starch, sucrose, maltose and cell wall components were significantly increased. The lack of both cPGM and pPGM activities in Arabidopsis resulted in dwarf growth, prematurely die off, and inability to develop a functional inflorescence. The combined results are discussed in comparison to potato, the only described mutant with lack of total PGM activity.     

Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing

Background

Plants selectively attract particular soil microorganisms, in particular consumers of root-excreted compounds. It is unclear to what extent cultivar type and/or growth stage affect this process.

Methodology/Principal Findings

DNA-based pyrosequencing was used to characterize the structure of bacterial communities in a field cropped with potato. The rhizospheres of six cultivars denoted Aveka, Aventra, Karnico, Modena, Premiere and Desiree, at three growth stages (young, flowering and senescence) were examined, in addition to corresponding bulk soils. Around 350,000 sequences were obtained (5,700 to 38,000 per sample). Across all samples, rank abundance distributions best fitted the power law model, which indicates a community composed of a few highly dominant species next to numerous rare species. Grouping of the sequences showed that members of the Actinobacteria, Alphaproteobacteria, next to as-yet-unclassified bacteria, dominated. Other groups that were consistently found, albeit at lower abundance, were Beta-, Gamma- and Deltaproteobacteria and Acidobacteria. Principal components analyses revealed that rhizosphere samples were significantly different from corresponding bulk soil in each growth stage. Furthermore, cultivar effects were found in the young plant stage, whereas these became insignificant in the flowering and senescence stages. Besides, an effect of time of season was observed for both rhizosphere and bulk soils. The analyzed rhizosphere samples of the potato cultivars were grouped into two groups, in accordance with the allocation of carbon to starch in their tubers, i.e. Aveka, Aventra and Karnico (high) versus Premiere and Desiree (low) and thus replicates per group were established.

Conclusions

Across all potato cultivars, the young plant stages revealed cultivar-dependent bacterial community structures, which disappeared in the flowering and senescence stages. Furthermore, Pseudomonas, Beta-, Alpha- and Deltaproteobacteria flourished under different ecological conditions than the Acidobacteria.     

Photosynthate metabolism in the source leaves of n(2)-fixing soybean plants

Soybean plants (Glycine max [L.] Merr. cv Williams), which were symbiotic with Bradyrhizobium japonicum, and which grew well upon reduced nitrogen supplied solely through N₂ fixation processes, often exhibited excess accumulation of starch and sucrose and diminished soluble protein in their source leaves. Nitrate and ammonia, when supplied to the nodulated roots of N₂-fixing plants, mediated a reduction of foliar starch accumulation and a corresponding increase in soluble protein in the source leaves. This provided an opportunity to examine the potential metabolic adjustments by which NO₃⁻ and NH₄⁺ (N) sufficiency or deficiency exerted an influence upon soybean leaf starch synthesis. When compared with soybean plants supplied with N, elevated starch accumulation was focused in leaf palisade parenchyma tissue of N₂-fixing plants. Foliar activities of starch synthesis pathway enzymes including fructose-1,6-bisphosphate phosphatase, phosphohexoisomerase, phosphoglucomutase (PGM), as well as adenosine diphosphate glucose pyrophosphorylase (in some leaves) exhibited highest activities in leaf extracts of N₂-fixing plants when expressed on a leaf protein basis. This was interpreted to mean that there was an adaptation of these enzyme activities in the leaves of N₂-fixing plants, and this contributed to an increase in starch accumulation. Another major causal factor associated with increased starch accumulation was the elevation in foliar levels of fructose-6-phosphate, glucose-6-phosphate, and glucose-1-phosphate (G1P), which had risen to chloroplast concentrations considerably in excess of the K_m values for their respective target enzymes associated with starch synthesis, e.g. elevated G1P with respect to adenosine diphosphate glucose pyrophosphorylase (ADPG-PPiase) binding sites. The cofactor glucose-1,6-bisphosphate (G1,6BP) was found to be obligate for maximal PGM activity in soybean leaf extracts of N₂-fixing as well as N-supplemented plants, and G1,6BP levels in N₂-fixing plant leaves was twice that of levels in N-supplied treatments. However the concentration of chloroplastic G1,6BP in illuminated leaves was computed to be saturating with respect to PGM in both N₂-fixing and N-supplemented plants. This suggested that the higher level of this cofactor in N₂-fixing plant leaves did not confer any higher PGM activation and was not a factor in higher starch synthesis rates. Relative to plants supplied with NO₃⁻ and NH₄⁺, the source leaf glycerate-3-phosphate (3-PGA) and orthophosphate (Pi) concentrations in leaves of N₂-fixing plants were two to four times higher. Although Pi is a physiological competitive inhibitor of leaf chloroplast ADPG-PPiase, and hence, starch synthesis, elevated chloroplast 3-PGA levels in N₂-fixing plant leaves apparently prevented interference of Pi with ADPG-PPiase catalysis and starch synthesis.     

Relating Mutant Genotype to Phenotype via Quantitative Behavior of the NADPH Redox Cycle in Human Erythrocytes

Background

The NADPH redox cycle plays a key role in antioxidant protection of human erythrocytes. It consists of two enzymes: glucose-6-phosphate dehydrogenase (G6PD) and glutathione reductase. Over 160 G6PD variants have been characterized and associated with several distinct clinical manifestations. However, the mechanistic link between the genotype and the phenotype remains poorly understood.

Methodology/Principal Findings

We address this issue through a novel framework (design space) that integrates information at the genetic, biochemical and clinical levels. Our analysis predicts three qualitatively-distinct phenotypic regions that can be ranked according to fitness. When G6PD variants are analyzed in design space, a correlation is revealed between the phenotypic region and the clinical manifestation: the best region with normal physiology, the second best region with a pathology, and the worst region with a potential lethality. We also show that Plasmodium falciparum, by induction of its own G6PD gene in G6PD-deficient erythrocytes, moves the operation of the cycle to a region of the design space that yields robust performance.

Conclusions/Significance

In conclusion, the design space for the NADPH redox cycle, which includes relationships among genotype, phenotype and environment, illuminates the function, design and fitness of the cycle, and its phenotypic regions correlate with the organism''s clinical status.     

Highly diversified fungi are associated with the achlorophyllous orchid Gastrodia flavilabella

Background

Mycoheterotrophic orchids are achlorophyllous plants that obtain carbon and nutrients from their mycorrhizal fungi. They often show strong preferential association with certain fungi and may obtain nutrients from surrounding photosynthetic plants through ectomycorrhizal fungi. Gastrodia is a large genus of mycoheterotrophic orchids in Asia, but Gastrodia species’ association with fungi has not been well studied. We asked two questions: (1) whether certain fungi were preferentially associated with G. flavilabella, which is an orchid in Taiwan and (2) whether fungal associations of G. flavilabella were affected by the composition of fungi in the environment.

Results

Using next-generation sequencing, we studied the fungal communities in the tubers of Gastrodia flavilabella and the surrounding soil. We found (1) highly diversified fungi in the G. flavilabella tubers, (2) that Mycena species were the predominant fungi in the tubers but minor in the surrounding soil, and (3) the fungal communities in the G. flavilabella tubers were clearly distinct from those in the surrounding soil. We also found that the fungal composition in soil can change quickly with distance.

Conclusions

G. flavilabella was associated with many more fungi than previously thought. Among the fungi in the tuber of G. flavilabella, Mycena species were predominant, different from the previous finding that adult G. elata depends on Armillaria species for nutritional supply. Moreover, the preferential fungus association of G. flavilabella was not significantly influenced by the composition of fungi in the environment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1422-7) contains supplementary material, which is available to authorized users.