Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce

BackgroundCold acclimation in woody perennials is a metabolically intensive process, but coincides with environmental conditions that are not conducive to the generation of energy through photosynthesis. While the negative effects of low temperatures on the photosynthetic apparatus during winter have been well studied, less is known about how this is reflected at the level of gene and metabolite expression, nor how the plant generates primary metabolites needed for adaptive processes during autumn.ResultsThe MapMan tool revealed enrichment of the expression of genes related to mitochondrial function, antioxidant and associated regulatory activity, while changes in metabolite levels over the time course were consistent with the gene expression patterns observed. Genes related to thylakoid function were down-regulated as expected, with the exception of plastid targeted specific antioxidant gene products such as thylakoid-bound ascorbate peroxidase, components of the reactive oxygen species scavenging cycle, and the plastid terminal oxidase. In contrast, the conventional and alternative mitochondrial electron transport chains, the tricarboxylic acid cycle, and redox-associated proteins providing reactive oxygen species scavenging generated by electron transport chains functioning at low temperatures were all active.ConclusionsA regulatory mechanism linking thylakoid-bound ascorbate peroxidase action with “chloroplast dormancy” is proposed. Most importantly, the energy and substrates required for the substantial metabolic remodeling that is a hallmark of freezing acclimation could be provided by heterotrophic metabolism.

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title: A Molecular Timetable for Apical Bud Formation and Dormancy Induction in Poplar[W]
abstract: The growth of perennial plants in the temperate zone alternates with periods of dormancy that are typically initiated during bud development in autumn. In a systems biology approach to unravel the underlying molecular program of apical bud development in poplar (Populus tremula × Populus alba), combined transcript and metabolite profiling were applied to a high-resolution time course from short-day induction to complete dormancy. Metabolite and gene expression dynamics were used to reconstruct the temporal sequence of events during bud development. Importantly, bud development could be dissected into bud formation, acclimation to dehydration and cold, and dormancy. To each of these processes, specific sets of regulatory and marker genes and metabolites are associated and provide a reference frame for future functional studies. Light, ethylene, and abscisic acid signal transduction pathways consecutively control bud development by setting, modifying, or terminating these processes. Ethylene signal transduction is positioned temporally between light and abscisic acid signals and is putatively activated by transiently low hexose pools. The timing and place of cell proliferation arrest (related to dormancy) and of the accumulation of storage compounds (related to acclimation processes) were established within the bud by electron microscopy. Finally, the identification of a large set of genes commonly expressed during the growth-to-dormancy transitions in poplar apical buds, cambium, or Arabidopsis thaliana seeds suggests parallels in the underlying molecular mechanisms in different plant organs.

title: Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks.
abstract: We have performed transcript and metabolite profiling of isolated cambial meristem cells of the model tree aspen during the course of their activity-dormancy cycle to better understand the environmental and hormonal regulation of this process in perennial plants. Considerable modulation of cambial transcriptome and metabolome occurs throughout the activity-dormancy cycle. However, in addition to transcription, post-transcriptional control is also an important regulatory mechanism as exemplified by the regulation of cell-cycle genes during the reactivation of cambial cell division in the spring. Genes related to cold hardiness display temporally distinct induction patterns in the autumn which could explain the step-wise development of cold hardiness. Factors other than low temperature regulate the induction of early cold hardiness-related genes whereas abscisic acid (ABA) could potentially regulate the induction of late cold hardiness-related genes in the autumn. Starch breakdown in the autumn appears to be regulated by the 'short day' signal and plays a key role in providing substrates for the production of energy, fatty acids and cryoprotectants. Catabolism of sucrose and fats provides energy during the early stages of reactivation in the spring, whereas the reducing equivalents are generated through activation of the pentose phosphate shunt. Modulation of gibberellin (GA) signaling and biosynthesis could play a key role in the regulation of cambial activity during the activity-dormancy cycle as suggested by the induction of PttRGA which encodes a negative regulator of growth in the autumn and that of a GA-20 oxidase, a key gibberellin biosynthesis gene during reactivation in spring. In summary, our data reveal the dynamics of transcriptional and metabolic networks and identify potential targets of environmental and hormonal signals in the regulation of the activity-dormancy cycle in cambial meristem.

title: Correlating gene expression to physiological parameters and environmental conditions during cold acclimation of Pinus sylvestris, identification of molecular markers using cDNA microarrays.
abstract: Scots pine (Pinus sylvestris L.) seedlings were grown under different conditions (three field locations, two seasons and two climate room regimes), and then analyzed for freezing tolerance of shoots and roots and for transcript abundance in apical buds based on a cDNA microarray containing about 1500 expressed sequence tags (ESTs) from buds of cold-treated Scots pine seedlings. In a climate room providing long daily photoperiods and high temperatures, seedlings did not develop freezing tolerance, whereas seedlings in a climate room set to provide declining temperatures and day lengths developed moderate freezing tolerance. Control seedlings grown outside under field conditions developed full freezing tolerance. Differences in physiological behavior of the different seedling groups, combined with molecular analysis, allowed identification of a large group of genes, expression of which changed during the development of freezing tolerance. Transcript abundance of several of these genes was highly correlated with freezing tolerance in seedlings differing in provenance, field location or age, making them excellent candidate marker genes for molecular tests for freezing tolerance.

title: Populus CEN/TFL1 regulates first onset of flowering, axillary meristem identity and dormancy release in Populus.
abstract: Members of the CENTRORADIALIS (CEN)/TERMINAL FLOWER 1 (TFL1) subfamily control shoot meristem identity, and loss-of-function mutations in both monopodial and sympodial herbaceous plants result in dramatic changes in plant architecture. We studied the degree of conservation between herbaceous and woody perennial plants in shoot system regulation by overexpression and RNA interference (RNAi)-mediated suppression of poplar orthologs of CEN, and the related gene MOTHER OF FT AND TFL 1 (MFT). Field study of transgenic poplars (Populus spp.) for over 6 years showed that downregulation of PopCEN1 and its close paralog, PopCEN2, accelerated the onset of mature tree characteristics, including age of first flowering, number of inflorescences and proportion of short shoots. Surprisingly, terminal vegetative meristems remained indeterminate in PopCEN1-RNAi trees, suggesting the possibility that florigen signals are transported to axillary mersitems rather than the shoot apex. However, the axillary inflorescences (catkins) of PopCEN1-RNAi trees contained fewer flowers than did wild-type catkins, suggesting a possible role in maintaining the indeterminacy of the inflorescence apex. Expression of PopCEN1 was significantly correlated with delayed spring bud flush in multiple years, and in controlled environment experiments, 35S::PopCEN1 and RNAi transgenics required different chilling times to release dormancy. Considered together, these results indicate that PopCEN1/PopCEN2 help to integrate shoot developmental transitions that recur during each seasonal cycle with the age-related changes that occur over years of growth.

title: CENL1 Expression in the Rib Meristem Affects Stem Elongation and the Transition to Dormancy in Populus[W][OA]
abstract: We investigated the short day (SD)–induced transition to dormancy in wild-type hybrid poplar (Populus tremula × P. tremuloides) and its absence in transgenic poplar overexpressing heterologous PHYTOCHROME A (PHYA). CENTRORADIALIS-LIKE1 (CENL1), a poplar ortholog of Arabidopsis thaliana TERMINAL FLOWER1 (TFL1), was markedly downregulated in the wild-type apex coincident with SD-induced growth cessation. By contrast, poplar overexpressing a heterologous Avena sativa PHYA construct (P35S:AsPHYA), with PHYA accumulating in the rib meristem (RM) and adjacent tissues but not in the shoot apical meristem (SAM), upregulated CENL1 in the RM area coincident with an acceleration of stem elongation. In SD-exposed heterografts, both P35S:AsPHYA and wild-type scions ceased growth and formed buds, whereas only the wild type assumed dormancy and P35S:AsPHYA showed repetitive flushing. This shows that the transition is not dictated by leaf-produced signals but dependent on RM and SAM properties. In view of this, callose-enforced cell isolation in the SAM, associated with suspension of indeterminate growth during dormancy, may require downregulation of CENL1 in the RM. Accordingly, upregulation of CENL1/TFL1 might promote stem elongation in poplar as well as in Arabidopsis during bolting. Together, the results suggest that the RM is particularly sensitive to photoperiodic signals and that CENL1 in the RM influences transition to dormancy in hybrid poplar.

title: Photosynthesis of overwintering evergreen plants.
abstract: In this review we focus on photosynthetic behavior of overwintering evergreens with an emphasis on both the acclimative responses of photosynthesis to cold and the winter behavior of photosynthesis in conifers. Photosynthetic acclimation is discussed in terms of the requirement for a balance between the energy absorbed through largely temperature-insensitive photochemical processes and the energy used for temperature-sensitive biochemical processes and growth. Cold acclimation transforms the xanthophyll-mediated nonphotochemical antenna quenching of absorbed light from a short-term dynamic response to a long-term sustained quenching for the whole winter period. This acclimative response helps protect the evergreen foliage from photooxidative damage during the winter when photosynthesis is restricted or prevented by low temperatures. Although the molecular mechanisms behind the sustained winter excitation quenching are largely unknown, it does involve major alterations in the organization and composition of the photosystem II antenna. In addition, photosystem I may play an important role in overwintering evergreens not only by quenching absorbed light photochemically via its support of cyclic electron transport at low temperatures, but also by nonphotochemical quenching of absorbed light irrespective of temperature. The possible role of photosystem II reaction centers in nonphotochemical quenching of absorbed energy in overwintering evergreens is also discussed. Processes like chlororespiration and cyclic electron transport may also be important for maintaining the functional integrity of the photosynthetic apparatus of overwintering evergreens both during periods of thawing in winter and during recovery from winter stress in spring. We suggest that the photosynthetic acclimation responses of overwintering evergreens represent specific evolutionary adaptations for plant species that invest in the long-term maintenance of leaf structure in cold climatic zones as exemplified by the boreal forests of the Northern Hemisphere.

title: Photoinhibition of photosystem I
abstract: Photosystem I (PSI) is a large pigment-protein complex consisting of about 18 different subunits in plants. Recently, the structure of PSI isolated from pea was solved by X-ray crystallography at a resolution of 4.4 A (Ben-Shem et al. 2003). This work has highlighted the structural similarities and differences between plant PSI and cyanobacterial PSI, where a 2.5 A structure was published earlier (Jordan et al. 2001). The subunits of PSI are traditionally divided into 14 core subun its—most of which are also found in cyanobacte ria—and four homologous light harvesting complex I (LHCI) subunits, which are specific to plants . Under certain conditions, other LHCI subunits can be seen—at least in Arabidopsis (Klimmek et al. 2005). The PSI complex binds about 167 chlorophyll molecules (Ben-shem et al. 2003). A special pair of chlorophyll a molecules constitutes the P700 reaction center and

title: Regulation of energy partitioning and alternative electron transport pathways during cold acclimation of lodgepole pine is oxygen dependent.
abstract: Second year needles of Lodgepole pine (Pinus contorta L.) were exposed for 6 weeks to either simulated control summer ['summer'; 25 °C/250 photon flux denisty (PFD)], autumn ('autumn'; 15°C/250 PFD) or winter conditions ('winter'; 5 °C/250 PFD). We report that the proportion of linear electron transport utilized in carbon assimilation (ETR(CO2)) was 40% lower in both 'autumn' and 'winter' pine when compared with the 'summer' pine. In contrast, the proportion of excess photosynthetic linear electron transport (ETR(excess)) not used for carbon assimilation within the total ETR(Jf) increased by 30% in both 'autumn' and 'winter' pine. In 'autumn' pine acclimated to 15°C, the increased amounts of 'excess' electrons were directed equally to 21  kPa O2-dependent and 2  kPa O2-dependent alternative electron transport pathways and the fractions of excitation light energy utilized by PSII photochemistry (Φ(PSII)), thermally dissipated through Φ(NPQ) and dissipated by additional quenching mechanism(s) (Φ(f,D)) were similar to those in 'summer' pine. In contrast, in 'winter' needles acclimated to 5 °C, 60% of photosynthetically generated 'excess' electrons were utilized through the 2  kPa O2-dependent electron sink and only 15% by the photorespiratory (21  kPa O2) electron pathway. Needles exposed to 'winter' conditions led to a 3-fold lower Φ(PSII), only a marginal increase in Φ(NPQ) and a 2-fold higher Φ(f,D), which was O2 dependent compared with the 'summer' and 'autumn' pine. Our results demonstrate that the employment of a variety of alternative pathways for utilization of photosynthetically generated electrons by Lodgepole pine depends on the acclimation temperature. Furthermore, dissipation of excess light energy through constitutive non-photochemical quenching mechanisms is O2 dependent.

title: Photoprotective Strategies of Overwintering Evergreens
abstract: High levels of solar radiation (direct and reflected off snow) can be absorbed by green leaves in the winter. However, the energy that is absorbed by these leaves often cannot be used through photosynthesis under winter conditions. Most colored objects would simply bleach if faced with the same conditions, because light-absorbing pigments pass energy on to oxygen, forming reactive oxygen species that destroy the pigments. Two key means by which overwintering leaves prevent reactive oxygen-mediated damage have been identified. One, used by all leaves in the winter, involves the employment of xanthophyll carotenoids in a photoprotective process whereby the light energy absorbed by chlorophyll is converted to heat and dissipated harmlessly. The other, found in some evergreen species but not in overwintering annual or biennial mesophytes, involves the degradation of proteins responsible for generating high-energy electrons, thereby suppressing transfer of these electrons to oxygen.

title: Excitation energy partitioning and quenching during cold acclimation in Scots pine.
abstract: We studied the influence of two irradiances on cold acclimation and recovery of photosynthesis in Scots pine (Pinus sylvestris L.) seedlings to assess mechanisms for quenching the excess energy captured by the photosynthetic apparatus. A shift in temperature from 20 to 5 degrees C caused a greater decrease in photosynthetic activity, measured by chlorophyll fluorescence and oxygen evolution, in plants exposed to moderate light (350 micromol m(-2) s(-1)) than in shaded plants (50 micromol m(-2) s(-1)). In response to the temperature shift, maximal photochemical efficiency of photosystem II (PSII), measured as the ratio of variable to maximal chlorophyll fluorescence (Fv/Fm) of dark-adapted samples, decreased to 70% in exposed seedlings, whereas shaded seedlings maintained Fv/Fm close to initial values. After a further temperature decrease to -5 degrees C, only 8% of initial Fv/Fm remained in exposed plants, whereas shaded plants retained 40% of initial Fv/Fm. Seven days after transfer from -5 to 20 degrees C, recovery of photochemical efficiency was more complete in the shaded plants than in the exposed plants (87 and 65% of the initial Fv/Fm value, respectively). In response to cold stress, the estimated functional absorption cross section per remaining PSII reaction center increased at both irradiances, but the increase was more pronounced in exposed seedlings. Estimates of energy partitioning in the needles showed a much higher dissipative component in the exposed seedlings at low temperatures, pointing to stronger development of non-photochemical quenching at moderate irradiances. The de-epoxidation state of the xanthophyll cycle pigments increased in exposed seedlings at 5 degrees C, contributing to the quenching capacity, whereas significant de-epoxidation in the shaded plants was observed only when temperatures decreased to -5 degrees C. Thermoluminescence (TL) measurements of PSII revealed that charge recombinations between the second oxidation state of Mn-cluster S2 and the semireduced secondary electron acceptor quinone Q(B)- (S2Q(B)-) were shifted to lower temperatures in cold-acclimated seedlings compared with control seedlings and this effect depended on irradiance. Concomitant with this, cold-acclimated seedlings demonstrated a significant shift in the S2 recombination with primary acceptor Q(A)- (S2Q(A)-) characteristic TL emission peak to higher temperatures, thus narrowing the redox potential gap between S2Q(B)- and S2Q(A)-, which might result in increased probability for non-radiative radical pair recombination between the PSII reaction center chlorophyll a (P680+) and Q(A)- (P680+)Q(A)-) (reaction center quenching) in cold-acclimated seedlings. In Scots pine seedlings, mechanisms of quenching excess light energy in winter therefore involve light-dependent regulation of reaction center content and both reaction center-based and antenna-based quenching of excess light energy, enabling them to withstand high excitation pressure under northern winter conditions.

title: Photosynthetic activity in winter needles of the evergreen tree Taxus cuspidata at low temperatures.
abstract: Photosystems harvest light energy, yet this energy cannot be efficiently employed for CO(2) assimilation at the below-freezing temperatures to which plants are typically exposed during winter in the temperate and boreal zones. To elucidate the mechanisms whereby this energy is dissipated, I evaluated performance of photosystems in winter needles of the evergreen tree Taxus cuspidata Sieb. et Zucc. Chloroplasts were localized adjacent to plasma membranes in needle cells in summer, whereas they congregated together in the centers of the cells during winter. When winter needles were acclimated to a temperature of 20 degrees C, their chloroplasts gradually dispersed to the edges of the cells, as in the summer. Acclimation-dependent relocalization coincided with changes in CO(2) uptake. Examination of photosystem II fluorescence kinetics in winter needles indicated that the quinone electron acceptor (Q(A)) reduction rate exceeded the Q(A) oxidation rate at low temperatures. The majority of Q(A) remained reduced even when winter needles were subjected to a temperature of -5 degrees C at low irradiance.

title: Photosystem II reaction centre quenching: mechanisms and physiological role
abstract: Dissipation of excess absorbed light energy in eukaryotic photoautotrophs through zeaxanthin- and ΔpH-dependent photosystem II antenna quenching is considered the major mechanism for non-photochemical quenching and photoprotection. However, there is mounting evidence of a zeaxanthin-independent pathway for dissipation of excess light energy based within the PSII reaction centre that may also play a significant role in photoprotection. We summarize recent reports which indicate that this enigma can be explained, in part, by the fact that PSII reaction centres can be reversibly interconverted from photochemical energy transducers that convert light into ATP and NADPH to efficient, non-photochemical energy quenchers that protect the photosynthetic apparatus from photodamage. In our opinion, reaction centre quenching complements photoprotection through antenna quenching, and dynamic regulation of photosystem II reaction centre represents a general response to any environmental condition that predisposes the accumulation of reduced QA in the photosystem II reaction centres of prokaryotic and eukaryotic photoautotrophs. Since the evolution of reaction centres preceded the evolution of light harvesting systems, reaction centre quenching may represent the oldest photoprotective mechanism.

title: Two different strategies for light utilization in photosynthesis in relation to growth and cold acclimation
abstract: Seedlings of Lodgepole pine (Pinus contorta L.) and winter wheat (Triticum aestivum L. cv. Monopol) were cold acclimated under controlled conditions to induce frost hardiness. Lodgepole pine responded to cold acclimation by partial inhibition of photosynthesis with an associated partial loss of photosystem II reaction centres, and a reduction in needle chlorophyll content. This was accompanied by a low daily carbon gain, and the development of a high and sustained capacity for non-photochemical quenching of absorbed light. This sustained dissipation of absorbed light as heat correlated with an increased de-epoxidation of the xanthophyll cycle pigments forming the quenching forms antheraxanthin and zeaxanthin. In addition, the PsbS protein known to bind chlorophyll and the xanthophyll cycle pigments increased strongly during cold acclimation of pine. In contrast, winter wheat maintained high photosynthetic rates, showed no loss of chlorophyll content per leaf area, and exhibited a high daily carbon gain and a minimal non-photochemical quenching after cold acclimation. In accordance, cold acclimation of wheat neither increased the de-epoxidation of the xanthophylls nor the content of the PsbS protein. These different responses of photosynthesis to cold acclimation are correlated with pine, reducing its need for assimilates when entering dormancy associated with termination of primary growth, whereas winter wheat maintains a high need for assimilates as it continues to grow and develop throughout the cold-acclimation period. It appears that without evolving a sustained ability for controlled dissipation of absorbed light as heat throughout the winter, winter green conifers would not have managed to adapt and establish themselves so successfully in the cold climatic zones of the northern hemisphere.

title: Seasonal changes in abundance and phosphorylation status of photosynthetic proteins in eastern white pine and balsam fir.
abstract: During winter, the light-harvesting complexes of evergreen plants change function from energy-harvesting to energy-dissipating centers. The goal of our study was to monitor changes in the composition of the photosynthetic apparatus that accompany these functional changes. Seasonal changes in chlorophyll fluorescence, pigment concentration, and abundance and phosphorylation status of photosynthetic proteins in Pinus strobus L. (sun-exposed trees) and Abies balsamea (L.) P. Mill. (sun-exposed and shaded trees) were examined in the cold winter climate of Minnesota. Results indicated typical seasonal changes in chlorophyll fluorescence and pigment concentration, with sustained reduced photosystem II (PSII) efficiency during winter, accompanied by retention of zeaxanthin and antheraxanthin, and winter increases in the pool of xanthophyll cycle pigments and lutein. In sun-exposed trees, all photosynthetic proteins that were monitored decreased in relative abundance during winter, although two light-harvesting chlorophyll a/b binding proteins (Lhcb2 and Lhcb5), and the PsbS protein, were enriched in non-summer months, suggesting a role for these proteins in winter acclimation. In contrast, shaded trees maintained most of their protein throughout winter, with reductions occurring in spring. Thylakoid protein phosphorylation data suggest winter increases in the phosphorylation of a PSII core protein, PsbH, in sun-exposed trees, and increases in phosphorylation of all PSII core proteins in shaded trees.

title: Acclimation to temperature and irradiance modulates PSII charge recombination
abstract: Acclimation of wild type and the chlorina F2 mutant of barley to either high light or low temperature results in a 2‐ to 3‐fold increase in non‐photochemical quenching which occurred independently of either energy‐dependent quenching (qE), xanthophyll cycle‐mediated antenna quenching or state transitions. Results of in vivo thermoluminescence measurements used to address this conundrum indicated that excitation pressure regulates the temperature gap for S 2 Q B ‐ and S 2 Q A ‐ charge recombinations within photosystem II reaction centers. This is discussed in terms of photoprotection through non‐radiative charge recombination.

title: Characterization of the photosynthetic apparatus in cortical bark chlorenchyma of Scots pine
abstract: Winter-induced inhibition of photosynthesis in Scots pine (Pinus sylvestris L.) needles is accompanied by a 65% reduction of the maximum photochemical efficiency of photosystem II (PSII), measured as Fv/Fm, but relatively stable photosystem I (PSI) activity. In contrast, the photochemical efficiency of PSII in bark chlorenchyma of Scots pine twigs was shown to be well preserved, while PSI capacity was severely decreased. Low-temperature (77 K) chlorophyll fluorescence measurements also revealed lower relative fluorescence intensity emitted from PSI in bark chlorenchyma compared to needles regardless of the growing season. Nondenaturating SDS-PAGE analysis of the chlorophyll–protein complexes also revealed much lower abundance of LHCI and the CPI band related to light harvesting and the core complex of PSI, respectively, in bark chlorenchyma. These changes were associated with a 38% reduction in the total amount of chlorophyll in the bark chlorenchyma relative to winter needles, but the Chl a/b ratio and carotenoid composition were similar in the two tissues. As distinct from winter pine needles exhibiting ATP/ADP ratio of 11.3, the total adenylate content in winter bark chlorenchyma was 2.5-fold higher and the estimated ATP/ADP ratio was 20.7. The photochemical efficiency of PSII in needles attached to the twig recovered significantly faster (28–30 h) then in detached needles. Fluorescence quenching analysis revealed a high reduction state of QA and the PQ-pool in the green bark tissue. The role of bark chlorenchyma and its photochemical performance during the recovery of photosynthesis from winter stress in Scots pine is discussed.

title: The IMMUTANS Variegation Locus of Arabidopsis Defines a Mitochondrial Alternative Oxidase Homolog That Functions during Early Chloroplast Biogenesis
abstract: Nuclear gene–induced variegation mutants provide a powerful system to dissect interactions between the genetic systems of the nucleus–cytoplasm, the chloroplast, and the mitochondrion. The immutans (im) variegation mutation of Arabidopsis is nuclear and recessive and results in the production of green- and white-sectored leaves. The green sectors contain cells with normal chloroplasts, whereas the white sectors are heteroplastidic and contain cells with abnormal, pigment-deficient plastids as well as some normal chloroplasts. White sector formation can be promoted by enhanced light intensities, but sectoring becomes irreversible early in leaf development. The white sectors accumulate the carotenoid precursor phytoene. We have positionally cloned IM and found that the gene encodes a 40.5-kD protein with sequence motifs characteristic of alternative oxidase, a mitochondrial protein that functions as a terminal oxidase in the respiratory chains of all plants. However, phylogenetic analyses revealed that the IM protein is only distantly related to these other alternative oxidases, suggesting that IM is a novel member of this protein class. We sequenced three alleles of im, and all are predicted to be null. Our data suggest a model of variegation in which the IM protein functions early in chloroplast biogenesis as a component of a redox chain responsible for phytoene desaturation but that a redundant electron transfer function is capable of compensating for IM activity in some plastids and cells.

title: Physiological roles of plastid terminal oxidase in plant stress responses
abstract: The plastid terminal oxidase (PTOX) is a plastoquinol oxidase localized in the plastids of plants. It is able to transfer electrons from plastoquinone (PQ) to molecular oxygen with the formation of water. Recent studies have suggested that PTOX is beneficial for plants under environmental stresses, since it is involved in the synthesis of photoprotective carotenoids and chlororespiration, which could potentially protect the chloroplast electron transport chain (ETC) from over-reduction. The absence of PTOX in plants usually results in photo-bleached variegated leaves and impaired adaptation to environment alteration. Although PTOX level and activity has been found to increase under a wide range of stress conditions, the functions of plant PTOX in stress responses are still disputed now. In this paper, the possible physiological roles of PTOX in plant stress responses are discussed based on the recent progress.

title: Chlororespiration and cyclic electron flow around PSI during photosynthesis and plant stress response.
abstract: Besides major photosynthetic complexes of oxygenic photosynthesis, new electron carriers have been identified in thylakoid membranes of higher plant chloroplasts. These minor components, located in the stroma lamellae, include a plastidial NAD(P)H dehydrogenase (NDH) complex and a plastid terminal plastoquinone oxidase (PTOX). The NDH complex, by reducing plastoquinones (PQs), participates in one of the two electron transfer pathways operating around photosystem I (PSI), the other likely involving a still uncharacterized ferredoxin-plastoquinone reductase (FQR) and the newly discovered PGR5. The existence of a complex network of mechanisms regulating expression and activity of the NDH complex, and the presence of higher amounts of NDH complex and PTOX in response to environmental stress conditions the phenotype of mutants, indicate that these components likely play a role in the acclimation of photosynthesis to changing environmental conditions. Based on recently published data, we propose that the NDH-dependent cyclic pathway around PSI participates to the ATP supply in conditions of high ATP demand (such as high temperature or water limitation) and together with PTOX regulates cyclic electron transfer activity by tuning the redox state of intersystem electron carriers. In response to severe stress conditions, PTOX associated to the NDH and/or the PGR5 pathway may also limit electron pressure on PSI acceptor and prevent PSI photoinhibition.

title: Connecting the plastid: transporters of the plastid envelope and their role in linking plastidial with cytosolic metabolism.
abstract: Plastids have a multitude of functions in eukaryotic cells, ranging from photosynthesis to storage, and a role in essential biosynthetic pathways. All plastids are of either primary or higher-order endosymbiotic origin. That is, either a photosynthetic cyanobacterium was integrated into a mitochondriate eukaryotic host cell (primary endosymbiosis) or a plastid-bearing eukaryotic cell merged with another eukaryotic cell (secondary or higher-order endosymbioses), thereby passing on the plastid between various eukaryotic lineages. For all of these endosymbioses to become functional, it was essential to establish metabolic connections between organelle and host cell. Here, we review the present understanding of metabolite exchange between plastids and the surrounding cytosol in the context of the endosymbiotic origin of plastids in various eukaryotic lineages. We show that only a small number of transporters that can be traced down to the primary endosymbiotic event are conserved between plastids of diverse origins.

title: Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants.
abstract: Various abiotic stresses lead to the overproduction of reactive oxygen species (ROS) in plants which are highly reactive and toxic and cause damage to proteins, lipids, carbohydrates and DNA which ultimately results in oxidative stress. The ROS comprises both free radical (O(2)(-), superoxide radicals; OH, hydroxyl radical; HO(2), perhydroxy radical and RO, alkoxy radicals) and non-radical (molecular) forms (H(2)O(2), hydrogen peroxide and (1)O(2), singlet oxygen). In chloroplasts, photosystem I and II (PSI and PSII) are the major sites for the production of (1)O(2) and O(2)(-). In mitochondria, complex I, ubiquinone and complex III of electron transport chain (ETC) are the major sites for the generation of O(2)(-). The antioxidant defense machinery protects plants against oxidative stress damages. Plants possess very efficient enzymatic (superoxide dismutase, SOD; catalase, CAT; ascorbate peroxidase, APX; glutathione reductase, GR; monodehydroascorbate reductase, MDHAR; dehydroascorbate reductase, DHAR; glutathione peroxidase, GPX; guaicol peroxidase, GOPX and glutathione-S- transferase, GST) and non-enzymatic (ascorbic acid, ASH; glutathione, GSH; phenolic compounds, alkaloids, non-protein amino acids and α-tocopherols) antioxidant defense systems which work in concert to control the cascades of uncontrolled oxidation and protect plant cells from oxidative damage by scavenging of ROS. ROS also influence the expression of a number of genes and therefore control the many processes like growth, cell cycle, programmed cell death (PCD), abiotic stress responses, pathogen defense, systemic signaling and development. In this review, we describe the biochemistry of ROS and their production sites, and ROS scavenging antioxidant defense machinery.

title: Transgenic Plant Cells Lacking Mitochondrial Alternative Oxidase Have Increased Susceptibility to Mitochondria-Dependent and -Independent Pathways of Programmed Cell Death1
abstract: The plant mitochondrial electron transport chain is branched such that electrons at ubiquinol can be diverted to oxygen via the alternative oxidase (AOX). This pathway does not contribute to ATP synthesis but can dampen the mitochondrial generation of reactive oxygen species. Here, we establish that transgenic tobacco (Nicotiana tabacum L. cv Petit Havana SR1) cells lacking AOX (AS8 cells) show increased susceptibility to three different death-inducing compounds (H2O2, salicylic acid [SA], and the protein phosphatase inhibitor cantharidin) in comparison with wild-type cells. The timing and extent of AS8 cell death are very similar among the three treatments and, in each case, are accompanied by the accumulation of oligonucleosomal fragments of DNA, indicative of programmed cell death. Death induced by H2O2 or SA occurs by a mitochondria-dependent pathway characterized by cytochrome c release from the mitochondrion. Conversely, death induced by cantharidin occurs by a pathway without any obvious mitochondrial involvement. The ability of AOX to attenuate these death pathways may relate to its ability to maintain mitochondrial function after insult with a death-inducing compound or may relate to its ability to prevent chronic oxidative stress within the mitochondrion. In support of the latter, long-term treatment of AS8 cells with an antioxidant compound increased the resistance of AS8 cells to SA- or cantharidin-induced death. The results indicate that plants maintain both mitochondria-dependent and -independent pathways of programmed cell death and that AOX may act as an important mitochondrial “survival protein” against such death.

title: Phosphite accelerates programmed cell death in phosphate-starved oilseed rape (Brassica napus) suspension cell cultures
abstract: Phosphite (H2PO3−, Phi) prevents the acclimation of plants and yeast to orthophosphate (Pi, HPO42−) deprivation by specifically obstructing the derepression of genes encoding proteins characteristic of their Pi-starvation response. In this study, we report that prolonged (i.e., 3–4 weeks) culture of Brassica napus L. suspension cells in Pi-deficient (−Pi) media leads to programmed cell death (PCD). However, when the B. napus cells were subcultured into −Pi media containing 2 mM Phi, they initiated PCD within 5 days, with 95% cell death observed by day 9. Dying cells exhibited several morphological and biochemical features characteristic of PCD, including protoplast shrinkage, chromatin condensation, and fragmentation of nuclear DNA. Immunoblotting indicated that B. napus cells undergoing PCD upregulated a 30-kDa cysteine endoprotease that is induced during PCD in the inner integument cells of developing B. napus seeds. It is concluded that PCD in B. napus suspension cells is triggered by extended Pi starvation, and that Phi treatment greatly accelerates this process. Our results also infer that the adaptive value of acclimating at the molecular level to Pi-stress is to extend the viability of −Pi B. napus cell cultures by about 3 weeks.

title: Short-term salinity stress in tobacco plants leads to the onset of animal-like PCD hallmarks in planta in contrast to long-term stress
abstract: Recent results have identified mitochondria as centers of stress-induced generation of reactive oxygen species in plants. Depolarization of plant mitochondrial membrane during stress results the release of programmed cell death (PCD)-inducing factors in the cytosol in a fashion similar to the onset of animal-like PCD. Herein, we report significant similarities of animal-like PCD and salinity stress-induced plant PCD. Short-term salinity stress (3 h) led to depolarization of the mitochondrial membrane, release of cytochrome c (CYT-c), which was visualized using a contemporary molecular technique, activation of caspase-3 type proteases and the onset of PCD in wild type tobacco plants, Nicotiana tabacum cv. Petit Havana. However, PCD was not manifested during long-term salinity stress (24 h). Interestingly long-term salinity stress led to necrotic-like features, which were accompanied by collapse of respiration, reduction of key components of the respiratory chain, such as CYT-c and alternative oxidase, ATP depletion and high proteolytic activity. The results suggest that salinity stress of tobacco plants in planta leads to the onset of animal-like PCD only during the early stages post-stress, while long-term stress leads to necrotic-like features.

title: Reactive oxygen species and temperature stresses: A delicate balance between signaling and destruction
abstract: Temperature stress can have a devastating effect on plant metabolism, disrupting cellular homeostasis, and uncoupling major physiological processes. A direct result of stress-induced cellular changes is the enhanced accumulation of toxic compounds in cells that include reactive oxygen species (ROS). Although a considerable amount of work has shown a direct link between ROS scavenging and plant tolerance to temperature stress, recent studies have shown that ROS could also play a key role in mediating important signal transduction events. Thus, ROS, such as superoxide (O2–), are produced by NADPH oxidases during abiotic stress to activate stress-response pathways and induce defense mechanisms. The rates and cellular sites of ROS production during temperature stress could play a central role in stress perception and protection. ROS levels, as well as ROS signals, are thought to be controlled by the ROS gene network of plants. It is likely that in plants this network is interlinked with the different networks that control temperature stress acclimation and tolerance. In this review paper, we attempt to summarize some of the recent studies linking ROS and temperature stress in plants and propose a model for the involvement of ROS in temperature stress sensing and defense.

title: Mitochondrial uncoupling protein is required for efficient photosynthesis
abstract: Uncoupling proteins (UCPs) occur in the inner mitochondrial membrane and dissipate the proton gradient across this membrane that is normally used for ATP synthesis. Although the catalytic function and regulation of plant UCPs have been described, the physiological purpose of UCP in plants has not been established. Here, biochemical and physiological analyses of an insertional knockout of one of the Arabidopsis UCP genes (AtUCP1) are presented that resolve this issue. Absence of UCP1 results in localized oxidative stress but does not impair the ability of the plant to withstand a wide range of abiotic stresses. However, absence of UCP1 results in a photosynthetic phenotype. Specifically there is a restriction in photorespiration with a decrease in the rate of oxidation of photorespiratory glycine in the mitochondrion. This change leads to an associated reduced photosynthetic carbon assimilation rate. Collectively, these results suggest that the main physiological role of UCP1 in Arabidopsis leaves is related to maintaining the redox poise of the mitochondrial electron transport chain to facilitate photosynthetic metabolism.

title: Arabidopsis thaliana Uncoupling Proteins (AtUCPs): insights into gene expression during development and stress response and epigenetic regulation
abstract: Mitochondrial inner membrane uncoupling proteins (UCP) catalyze a proton conductance that dissipates the proton electrochemical gradient established by the respiratory chain, thus affecting the yield of ATP synthesis. UCPs are involved in mitochondrial energy flow regulation and have been implicated in oxidative stress tolerance. Based on the global gene expression profiling datasets available for Arabidopsis thaliana, in this review we discuss the regulation of UCP gene expression during development and in response to stress, and provide interesting insights on the possible existence of epigenetic regulation of UCP expression.

title: The Functional Organization and Control of Plant Respiration
abstract: The respiratory pathways of glycolysis, the tricarboxylic acid (TCA) cycle, and mitochondrial electron transport chain (miETC) are central features of carbon metabolism and bioenergetics in aerobic organisms. Respiration is essential for growth, maintenance, and carbon balance of all plant cells. Although the majority of respiratory enzymes are common to all organisms, plant respiration has evolved as a complex metabolic network endowed with a wide variety of unique characteristics. Plants have the option of employing alternative enzymes that bypass several of the conventional steps in cytosolic glycolysis, the TCA cycle, and miETC. The extent and conditions under which these bypasses operate is the subject of intensive research. The highly flexible nature of respiratory metabolism in plants has likely evolved in response to the crucial biosynthetic role played by respiration beyond its role in ATP generation; both functions must proceed if plants are to survive under varying and often stressful environmental and nutritional conditions. Additional complexity arises due to the existence of tissue- and/or developmental-specific isozymes of many plant respiratory enzymes, as well as the extensive interactions between photosynthesis and respiration, and plastidic, cytosolic, and mitochondrial metabolism in general. Recent progress in biochemistry, physiology, cell biology, genomics, transcriptomics, proteomics, metabolomics, and in vivo flux analyses have resulted in exciting new insights into many aspects of plant respiratory metabolism. Experiments on transgenic or mutant plants possessing significantly elevated or reduced levels of respiratory enzymes are augmenting our understanding of the functions, organization, and control of plant respiration. Metabolic engineering of plant respiration is of significant practical interest as it provides both an important approach to enhancing crop yields, as well as a potential mechanism for mitigating global climate change due to elevated atmospheric CO 2 levels. Referee: Dr. Greg C. Vanlerberghe, University of Toronto at Scarborough, Department of Life Sciences and Department of Botany, 1265 Military Trail, Scarborough, ON Canada M1C 1A4

title: Regulation of respiration in plants: a role for alternative metabolic pathways.
abstract: Respiratory metabolism includes the reactions of glycolysis, the tricarboxylic acid cycle and the mitochondrial electron transport chain, but is also directly linked with many other metabolic pathways such as protein and lipid biosynthesis and photosynthesis via photorespiration. Furthermore, any change in respiratory activity can impact the redox status of the cell and the production of reactive oxygen species. In this review, it is discussed how respiration is regulated and what alternative pathways are known that increase the metabolic flexibility of this vital metabolic process. By looking at the adaptive responses of respiration to hypoxia or changes in the oxygen availability of a cell, the integration of regulatory responses of various pathways is illustrated.

title: The Alternative Oxidase of Plant Mitochondria Is Involved in the Acclimation of Shoot Growth at Low Temperature. A Study of Arabidopsis AOX1a Transgenic Plants1[W]
abstract: The alternative oxidase (AOX) pathway of plant mitochondria uncouples respiration from mitochondrial ATP production and may ameliorate plant performance under stressful environmental conditions, such as cold temperatures, by preventing excess accumulation of reactive oxygen species. We tested this model in whole tissues by growing AtAOX1a-transformed Arabidopsis (Arabidopsis thaliana) plants at 12°C. For the first time, to our knowledge, in plants genetically engineered for AOX, we identified a vegetative shoot growth phenotype. Compared with wild type at day 21 after sowing, anti-sense and overexpressing lines showed, on average, 27% reduced leaf area and 25% smaller rosettes versus 30% increased leaf area and 33% larger rosette size, respectively. Lines overexpressing a mutated, constitutively active AOX1a showed smaller phenotypic effects. These phenotypic differences were not the result of a major alteration of the tissue redox state because the changes in levels of lipid peroxidation products, reflecting oxidative damage, and the expression of genes encoding antioxidant and electron transfer chain redox enzymes did not correspond with the shoot phenotypes. However, the observed phenotypes were correlated with the amount of total shoot anthocyanin at low temperature and with the transcription of the flavonoid pathway genes PAL1 and CHS. These results demonstrate that (1) AOX activity plays a role in shoot acclimation to low temperature in Arabidopsis, and that (2) AOX not only functions to prevent excess reactive oxygen species formation in whole tissues under stressful environmental conditions but also affects metabolism through more pervasive effects, including some that are extramitochondrial.

title: Overexpression of wheat alternative oxidase gene Waox1a alters respiration capacity and response to reactive oxygen species under low temperature in transgenic Arabidopsis.
abstract: Under low temperature conditions, the cytochrome pathway of respiration is repressed and reactive oxygen species (ROS) are produced in plants. Mitochondrial alternative oxidase (AOX) is the terminal oxidase responsible for the cyanide-insensitive and salicylhydroxamic acid-sensitive respiration. To study functions of wheat AOX genes under low temperature, we produced transgenic Arabidopsis by introducing Waox1a expressed under control of the cauliflower mosaic virus (CaMV) 35S promoter in Arabidopsis thaliana. The enhancement of endogenous AOX1a expression via low temperature stress was delayed in the transgenic Arabidopsis. Recovery of the total respiration activity under low temperature occurred more rapidly in the transgenic plants than in the wild-type plants due to a constitutively increased alternative pathway capacity. Levels of ROS decreased in the transgenic plants under low temperature stress. These results support the hypothesis that AOX alleviates oxidative stress when the cytochrome pathway of respiration is inhibited under abiotic stress conditions.

title: Alternative oxidase involvement in cold stress response of Arabidopsis thaliana fad2 and FAD3+ cell suspensions altered in membrane lipid composition.
abstract: To investigate how the fatty acid composition of membrane lipids influences cell growth and mitochondrial respiration, in particular the expression and capacity of alternative oxidase (AOX), under cold stress, we used the Arabidopsis thaliana fad2 knockout and FAD3+ -overexpressing cultured cells lines affected in extrachloroplastic fatty acid desaturation activities. At 22 degrees C, fad2 mitochondria exhibited a low polyunsaturated fatty acid content and low protein to lipid ratio, while mitochondria from FAD3+ were enriched in linolenic acid and in total membrane protein. As a consequence, both mutants showed a higher membrane microviscosity than the wild type. After exposure to 9 degrees C, FAD3+ mitochondria exhibited lower microviscosity and lower rigidification upon a temperature downshift than fad2. Furthermore, the extent of reduction of cell growth and respiratiory rates in the phosphorylating state was positively related to the cold sensitivity of each cell line, being more pronounced in fad2 that in the wild type, whereas the stability of those parameters reflected the cold resistance of FAD3+. In contrast, an increase in AOX capacity was observed in the three cell lines at 9 degrees C. These inductions were correlated to AOX protein amounts and seem to result from an accumulation of AOX1c transcripts in the three cell lines and of AOX1a transcripts in wild-type and fad2 cells. The fact that there is no direct relationship between the degree of cold tolerance of each cell line and their ability to enhance their AOX capacity suggests that the participation of AOX in the response of Arabidopsis cells to cold stress does not necessarily favor cold tolerance.

title: Involvement of hydrogen peroxide, calcium, and ethylene in the induction of the alternative pathway in chilling-stressed Arabidopsis callus
abstract: The roles of ethylene, hydrogen peroxide (H2O2), and calcium in inducing the capacity of the alternative respiratory pathway (AP) under chilling temperature in Arabidopsis thaliana calli were investigated. Exposure of wild-type (WT) calli, but not the calli of ethylene-insensitive mutants, etr1-3 and ein2-1, to chilling led to a marked increase of the AP capacity and triggered a rapid ethylene emission and H2O2 generation. Increasing ethylene emission by applying 1-aminocyclopropane-1-carboxylic (an ethylene precursor) markedly enhanced the AP capacity in WT calli, but not in etr1-3 and ein2-1 calli, whereas suppressing ethylene emission by applying aminooxyacetic acid (an ethylene biosynthesis inhibitor) abolished the chilling-induced AP capacity in WT calli. Furthermore, exogenous H2O2 treatment increased the AP capacity in WT calli, but not in etr1-3 and ein2-1 calli, while both catalase (H2O2 scavenger) and diphenylene iodonium (DPI, an inhibitor of NADPH oxidase) completely inhibited the chilling-induced H2O2 generation and largely inhibited the chilling-induced AP capacity. Interestingly, the chilling-induced AP capacity was completely inhibited by DPI and EGTA (calcium chelator). Further investigation demonstrated that H2O2 and calcium induced ethylene emission under chilling stress. Ethylene modulated the chilling-induced increase of pyruvate content and the expression of alternative oxidase genes (AOX1a and AOX1c). Taken together, these results indicate that H2O2-, calcium- and ethylene-dependent pathways are required for chilling-induced increase in AP capacity. However, only ethylene is indispensable for the activation of the AP capacity.

title: Alternative oxidase modulates leaf mitochondrial concentrations of superoxide and nitric oxide.
abstract: • The nonenergy-conserving alternative oxidase (AOX) has been hypothesized to modulate the amount of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in plant mitochondria but there is sparse direct in planta evidence to support this. • Laser scanning fluorescent confocal microscopy and biochemical methods were used to directly estimate in planta leaf concentrations of superoxide (O2(-)), nitric oxide (NO), peroxynitrite (ONOO(-)) and hydrogen peroxide (H(2)O(2)) in wildtype (Wt) tobacco (Nicotiana tabacum) and transgenic tobacco with altered amounts of AOX. • We found that plants lacking AOX have increased concentrations of leaf mitochondrial-localized O2(-) and leaf NO in comparison to the Wt, while leaf concentrations of H(2)O(2) were similar or lower in the AOX-suppressed plants. • Based on our results, we suggest that AOX respiration acts to reduce the generation of ROS and RNS in plant mitochondria by dampening the leak of single electrons from the electron transport chain to O(2) or nitrite. This may represent a universal role for AOX in plants. More work is now needed to establish the functional implications of this role, such as during abiotic and biotic stress.

title: The reduction of reactive oxygen species formation by mitochondrial alternative respiration in tomato basal defense against TMV infection
abstract: The role of mitochondrial alternative oxidase (AOX) and the relationship between systemic AOX induction, ROS formation, and systemic plant basal defense to Tobacco mosaic virus (TMV) were investigated in tomato plants. The results showed that TMV inoculation significantly increased the level of AOX gene transcripts, ubiquinone reduction levels, pyruvate content, and cyanide-resistant respiration (CN-resistant R) in upper, un-inoculated leaves. Pretreatment with potassium cyanide (KCN, a cytochrome pathway inhibitor) greatly increased CN-resistant R and reduced reactive oxygen species (ROS) formation, while application of salicylhydroxamic acid (SHAM, an AOX inhibitor) blocked the AOX activity and enhanced the production of ROS in the plants. Furthermore, TMV systemic infection was enhanced by SHAM and reduced by KCN pretreatment, as compared with the un-pretreated TMV counterpart. In addition, KCN application significantly diminished TMV-induced increase in antioxidant enzyme activities and dehydroascorbate/total ascorbate pool, while an opposite change was observed with SHAM-pretreated plants. These results suggest that the systemic induction of the mitochondrial AOX pathway plays a critical role in the reduction of ROS to enhance basal defenses. Additional antioxidant systems were also coordinately regulated in the maintenance of the cellular redox homeostasis.

title: Characterization of mitochondrial alternative NAD(P)H dehydrogenases in Arabidopsis: intraorganelle location and expression.
abstract: The intramitochondrial location of putative type II NAD(P)H dehydrogenases (NDs) in Arabidopsis was investigated by measuring the ability of isolated mitochondria to take up precursor proteins generated from cDNAs using an in vitro translation system. The mature proteins of NDA1, NDA2 and NDC1 were judged to be located on the inside of the inner membrane because they were protected from protease added after the mitochondrial outer membrane had been ruptured. In contrast, NDB1, NDB2 and NDB4 were not protected from protease digestion in mitochondria with ruptured outer membranes and were deemed to be located on the outside of the inner membrane. Expression of all ND genes was measured using quantitative reverse transcription-PCR (RT-PCR) to determine transcript abundance, and compared with expression of alternative oxidase, uncoupler proteins and selected components of the oxidative phosphorylation complexes. NDA1 and NDB2 were the most prominently expressed members in a variety of tissues, and were up-regulated in the early daytime in a diurnal manner. Analysis of array data suggested that NDA1 clustered closest to the gene encoding the P-subunit of glycine decarboxylase. Taken together with the diurnal regulation of NDA1 observed here and in other studies, this suggests that NDA1 plays a role in integrating metabolic activities of chloroplasts and mitochondria. NDA2, NDB2 and Aox1a were up-regulated in a coordinated manner under various treatments, potentially forming a complete respiratory chain capable of oxidizing matrix and cytosolic NAD(P)H. NDB1 and NDC1 were down-regulated under the same conditions and may be regarded as housekeeping genes.

title: Identification of AtNDI1, an Internal Non-Phosphorylating NAD(P)H Dehydrogenase in Arabidopsis Mitochondria1
abstract: Plant mitochondria contain non-phosphorylating NAD(P)H dehydrogenases (DHs) that are not found in animal mitochondria. The physiological function, substrate specificity, and location of enzymes within this family have yet to be conclusively determined. We have linked genome sequence information to protein and biochemical data to identify that At1g07180 (SwissProt Q8GWA1) from the Arabidopsis Genome Initiative database encodes AtNDI1, an internal NAD(P)H DH in Arabidopsis mitochondria. Three lines of evidence are presented: (a) The predicted protein sequence of AtNDI1 has high homology with other designated NAD(P)H DHs from microorganisms, (b) the capacity for matrix NAD(P)H oxidation via the rotenone-insensitive pathway is significantly reduced in the Atndi1 mutant plant line, and (c) the in vitro translation product of AtNDI1 is imported into isolated mitochondria and located on the inside of the inner membrane.

title: Alterations in the mitochondrial alternative NAD(P)H Dehydrogenase NDB4 lead to changes in mitochondrial electron transport chain composition, plant growth and response to oxidative stress.
abstract: The branched respiratory electron transport chain of plants contains a non-phosphorylating alternative pathway consisting of type II NAD(P)H dehydrogenases on both sides of the inner membrane linked through the ubiquinone pool to an alternative oxidase (AOX). T-DNA and RNA interference (RNAi) were used to reduce gene expression to characterize the external NAD(P)H dehydrogenase NDB4 in Arabidopsis. The ndb4 lines showed different levels of suppression of NDB4 protein, leading to increases in NBD2 and AOX1a mRNA and protein levels in all lines. These changes were associated with lower reactive oxygen species formation and an altered phenotype, including changes in growth rate, root : shoot ratios and leaf area. The general growth pattern for the ndb4 mutants was decreased leaf area early in development (6-15 d) followed by a prompt subsequent increase in leaf area that exceeded the leaf area of the wild type by maturity (the 10-12 rosette stage). This pattern was most evident for the RNAi lines that had increased mitochondrial electron transport capacity. The RNAi lines also exhibited better tolerance to salinity stress, with better growth rates and lower shoot Na⁺ content compared with controls when grown under saline conditions. We hypothesize that these differences reflect the enhanced expression of NDB2 and AOX in the ndb4 mutant plants.

title: Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis)
abstract: Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported a microarray study of the freezing acclimation period in Sitka spruce (Picea sitchensis) in which a large number of candidate genes for climatic adaptation were identified. In the current paper, we apply additional systems biology tools to these data to further probe changes in the levels of genes and metabolites and activities of associated pathways that regulate this complex developmental transition. One aspect of this adaptive process that is not well understood is the role of the cell wall. Our data suggest coordinated metabolic and signaling responses leading to cell wall remodeling. Co-expression of genes encoding proteins associated with biosynthesis of structural and non-structural cell wall carbohydrates was observed, which may be regulated by ethylene signaling components. At the same time, numerous genes, whose products are putatively localized to the endomembrane system and involved in both the synthesis and trafficking of cell wall carbohydrates, were up-regulated. Taken together, these results suggest a link between ethylene signaling and biosynthesis, and targeting of cell wall related gene products during the period of winter hardening. Automated Layout Pipeline for Inferred NEtworks (ALPINE), an in-house plugin for the Cytoscape visualization environment that utilizes the existing GeneMANIA and Mosaic plugins, together with the use of visualization tools, provided images of proposed signaling processes that became active over the time course of winter hardening, particularly at later time points in the process. The resulting visualizations have the potential to reveal novel, hypothesis-generating, gene association patterns in the context of targeted subcellular location.

title: Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis).
abstract: Cold acclimation in conifers is a complex process, the timing and extent of which reflects local adaptation and varies widely along latitudinal gradients for many temperate and boreal tree species. Despite their ecological and economic importance, little is known about the global changes in gene expression that accompany autumn cold acclimation in conifers. Using three populations of Sitka spruce (Picea sitchensis) spanning the species range, and a Picea cDNA microarray with 21,840 unique elements, within- and among-population gene expression was monitored during the autumn. Microarray data were validated for selected genes using real-time PCR. Similar numbers of genes were significantly twofold upregulated (1257) and downregulated (967) between late summer and early winter. Among those upregulated were dehydrins, pathogenesis-related/antifreeze genes, carbohydrate and lipid metabolism genes, and genes involved in signal transduction and transcriptional regulation. Among-population microarray hybridizations at early and late autumn time points revealed substantial variation in the autumn transcriptome, some of which may reflect local adaptation. These results demonstrate the complexity of cold acclimation in conifers, highlight similarities and differences to cold tolerance in annual plants, and provide a solid foundation for functional and genetic studies of this important adaptive process.

title: Plastid terminal oxidase (PTOX) has the potential to act as a safety valve for excess excitation energy in the alpine plant species Ranunculus glacialis L.
abstract: Ranunculus glacialis leaves were tested for their plastid terminal oxidase (PTOX) content and electron flow to photorespiration and to alternative acceptors. In shade-leaves, the PTOX and NAD(P)H dehydrogenase (NDH) content were markedly lower than in sun-leaves. Carbon assimilation/light and Ci response curves were not different in sun- and shade-leaves, but photosynthetic capacity was the highest in sun-leaves. Based on calculation of the apparent specificity factor of ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco), the magnitude of alternative electron flow unrelated to carboxylation and oxygenation of Rubisco correlated to the PTOX content in sun-, shade- and growth chamber-leaves. Similarly, fluorescence induction kinetics indicated more complete and more rapid reoxidation of the plastoquinone (PQ) pool in sun- than in shade-leaves. Blocking electron flow to assimilation, photorespiration and the Mehler reaction with appropriate inhibitors showed that sun-leaves were able to maintain higher electron flow and PQ oxidation. The results suggest that PTOX can act as a safety valve in R. glacialis leaves under conditions where incident photon flux density (PFD) exceeds the growth PFD and under conditions where the plastoquinone pool is highly reduced. Such conditions can occur frequently in alpine climates due to rapid light and temperature changes.

title: Implications of alternative electron sinks in increased resistance of PSII and PSI photochemistry to high light stress in cold-acclimated Arabidopsis thaliana
abstract: Exposure of control (non-hardened) Arabidopsis leaves to high light stress at 5 °C resulted in a decrease of both photosystem II (PSII) (45 %) and Photosystem I (PSI) (35 %) photochemical efficiencies compared to non-treated plants. In contrast, cold-acclimated (CA) leaves exhibited only 35 and 22 % decrease of PSII and PSI photochemistry, respectively, under the same conditions. This was accompanied by an accelerated rate of P700+ re-reduction, indicating an up-regulation of PSI-dependent cyclic electron transport (CET). Interestingly, the expression of the NDH-H gene and the relative abundance of the Ndh-H polypeptide, representing the NDH-complex, decreased as a result of exposure to low temperatures. This indicates that the NDH-dependent CET pathway cannot be involved and the overall stimulation of CET in CA plants is due to up-regulation of the ferredoxin–plastoquinone reductase, antimycin A-sensitive CET pathway. The lower abundance of NDH complex also implies lower activity of the chlororespiratory pathway in CA plants, although the expression level and overall abundance of the other well-characterized component involved in chlororespiration, the plastid terminal oxidase (PTOX), was up-regulated at low temperatures. This suggests increased PTOX-mediated alternative electron flow to oxygen in plants exposed to low temperatures. Indeed, the estimated proportion of O2-dependent linear electron transport not utilized in carbon assimilation and not directed to photorespiration was twofold higher in CA Arabidopsis. The possible involvement of alternative electron transport pathways in inducing greater resistance of both PSII and PSI to high light stress in CA plants is discussed.

title: Catalase function in plants: a focus on Arabidopsis mutants as stress-mimic models.
abstract: Hydrogen peroxide (H(2)O(2)) is an important signal molecule involved in plant development and environmental responses. Changes in H(2)O(2) availability can result from increased production or decreased metabolism. While plants contain several types of H(2)O(2)-metabolizing proteins, catalases are highly active enzymes that do not require cellular reductants as they primarily catalyse a dismutase reaction. This review provides an update on plant catalase genes, function, and subcellular localization, with a focus on recent information generated from studies on Arabidopsis. Original data are presented on Arabidopsis catalase single and double mutants, and the use of some of these lines as model systems to investigate the outcome of increases in intracellular H(2)O(2) are discussed. Particular attention is paid to interactions with cell thiol-disulphide status; the use of catalase-deficient plants to probe the apparent redundancy of reductive H(2)O(2)-metabolizing pathways; the importance of irradiance and growth daylength in determining the outcomes of catalase deficiency; and the induction of pathogenesis-related responses in catalase-deficient lines. Within the context of strategies aimed at understanding and engineering plant stress responses, the review also considers whether changes in catalase activities in wild-type plants are likely to be a significant part of plant responses to changes in environmental conditions or biotic challenge.

title: ROXY1, a member of the plant glutaredoxin family, is required for petal development in Arabidopsis thaliana
abstract: We isolated three alleles of an Arabidopsis thaliana gene named ROXY1, which initiates a reduced number of petal primordia and exhibits abnormalities during further petal development. The defects are restricted to the second whorl of the flower and independent of organ identity. ROXY1 belongs to a subgroup of glutaredoxins that are specific for higher plants and we present data on the first characterization of a mutant from this large Arabidopsis gene family for which information is scarce. ROXY1 is predominantly expressed in tissues that give rise to new flower primordia, including petal precursor cells and petal primordia. Occasionally, filamentous organs with stigmatic structures are formed in the second whorl of the roxy1 mutant, indicative for an ectopic function of the class C gene AGAMOUS (AG). The function of ROXY1 in the negative regulation of AG is corroborated by premature and ectopic AG expression in roxy1-3 ap1-10 double mutants, as well as by enhanced first whorl carpeloidy in double mutants of roxy1 with repressors of AG, such as ap2 or lug. Glutaredoxins are oxidoreductases that oxidize or reduce conserved cysteine-containing motifs. Mutagenesis of conserved cysteines within the ROXY1 protein demonstrates the importance of cysteine 49 for its function. Our data demonstrate that, unexpectedly, a plant glutaredoxin is involved in flower development, probably by mediating post-translational modifications of target proteins required for normal petal organ initiation and morphogenesis.

title: ROXY1 and ROXY2, two Arabidopsis glutaredoxin genes, are required for anther development.
abstract: Glutaredoxins (GRXs) are small oxidoreductases that are involved in various cellular processes and play a crucial role in responses to oxidative stress. Three GRX subgroups exist in plants, and GRXs with active sites of the CPYC and CGFS types are common to pro- and eukaryotes. In contrast, GRXs with the CC type motif have so far only been identified in land plants. Here, we report that the two CC-type GRXs ROXY1 and ROXY2 together control anther development in Arabidopsis thaliana. Single roxy1 and roxy2 mutants are fertile and produce normal anthers. However, roxy1 roxy2 double mutants are sterile and do not produce pollen. Strikingly, abaxial and adaxial anther lobe differentiation are differently affected, with early lobe differentiation being defective in the adaxial lobes, whereas later steps during pollen mother cell differentiation are disrupted in the abaxial lobes. Expression studies show that ROXY1 and ROXY2 are expressed with overlapping patterns during anther development. Lack of ROXY1 and ROXY2 function affects a large number of anther genes at the transcriptional level. Genetic and RT-PCR data imply that ROXY1/2 function downstream of the early-acting anther gene SPOROCYTELESS/NOZZLE and upstream of DYSFUNCTIONAL TAPETUM1, controlling tapetum development. Mutagenesis of a conserved glutathione-binding glycine in the ROXY1 protein indicates that CC-type GRXs need to interact with glutathione to catalyze essential biosynthetic reactions. Analysis of these two novel anther genes indicates that redox regulation, as well as participating in plant stress defense mechanisms, might play a major role in the control of male gametogenesis.

title: Nuclear Activity of ROXY1, a Glutaredoxin Interacting with TGA Factors, Is Required for Petal Development in Arabidopsis thaliana[W]
abstract: Glutaredoxins (GRXs) have thus far been associated mainly with redox-regulated processes participating in stress responses. However, ROXY1, encoding a GRX, has recently been shown to regulate petal primorida initiation and further petal morphogenesis in Arabidopsis thaliana. ROXY1 belongs to a land plant-specific class of GRXs that has a CC-type active site motif, which deviates from ubiquitously occurring CPYC and CGFS GRXs. Expression studies of yellow fluorescent protein-ROXY1 fusion genes driven by the cauliflower mosaic virus 35S promoter reveal a nucleocytoplasmic distribution of ROXY1. We demonstrate that nuclear localization of ROXY1 is indispensable and thus crucial for its activity in flower development. Yeast two-hybrid screens identified TGA transcription factors as interacting proteins, which was confirmed by bimolecular fluorescence complementation experiments showing their nuclear interaction in planta. Overlapping expression patterns of ROXY1 and TGA genes during flower development demonstrate that ROXY1/TGA protein interactions can occur in vivo and support their biological relevance in petal development. Deletion analysis of ROXY1 demonstrates the importance of the C terminus for its functionality and for mediating ROXY1/TGA protein interactions. Phenotypic analysis of the roxy1-2 pan double mutant and an engineered chimeric repressor mutant from PERIANTHIA (PAN), a floral TGA gene, supports a dual role of ROXY1 in petal development. Together, our results show that the ROXY1 protein functions in the nucleus, likely by modifying PAN posttranslationally and thereby regulating its activity in petal primordia initiation. Additionally, ROXY1 affects later petal morphogenesis, probably by modulating other TGA factors that might act redundantly during differentiation of second whorl organs.

title: Arabidopsis GLUTATHIONE REDUCTASE1 Plays a Crucial Role in Leaf Responses to Intracellular Hydrogen Peroxide and in Ensuring Appropriate Gene Expression through Both Salicylic Acid and Jasmonic Acid Signaling Pathways1[C][W][OA]
abstract: Glutathione is a major cellular thiol that is maintained in the reduced state by glutathione reductase (GR), which is encoded by two genes in Arabidopsis (Arabidopsis thaliana; GR1 and GR2). This study addressed the role of GR1 in hydrogen peroxide (H2O2) responses through a combined genetic, transcriptomic, and redox profiling approach. To identify the potential role of changes in glutathione status in H2O2 signaling, gr1 mutants, which show a constitutive increase in oxidized glutathione (GSSG), were compared with a catalase-deficient background (cat2), in which GSSG accumulation is conditionally driven by H2O2. Parallel transcriptomics analysis of gr1 and cat2 identified overlapping gene expression profiles that in both lines were dependent on growth daylength. Overlapping genes included phytohormone-associated genes, in particular implicating glutathione oxidation state in the regulation of jasmonic acid signaling. Direct analysis of H2O2-glutathione interactions in cat2 gr1 double mutants established that GR1-dependent glutathione status is required for multiple responses to increased H2O2 availability, including limitation of lesion formation, accumulation of salicylic acid, induction of pathogenesis-related genes, and signaling through jasmonic acid pathways. Modulation of these responses in cat2 gr1 was linked to dramatic GSSG accumulation and modified expression of specific glutaredoxins and glutathione S-transferases, but there is little or no evidence of generalized oxidative stress or changes in thioredoxin-associated gene expression. We conclude that GR1 plays a crucial role in daylength-dependent redox signaling and that this function cannot be replaced by the second Arabidopsis GR gene or by thiol systems such as the thioredoxin system.

title: Overexpression of thylakoidal ascorbate peroxidase shows enhanced resistance to chilling stress in tomato.
abstract: Photosynthesis provides a strong reducing power and a high risk for generation of reactive oxygen species (ROS) particularly under chilling stress. Ascorbate peroxidases (APXs) reduce H(2)O(2) to water and play an important role in the antioxidant system of plants. Though thylakoid ascorbate peroxidase (tAPX) has been thought to be key regulator of intracellular levels of H(2)O(2), its physiological significance in the response to chilling stress is still under discussion. To study the contribution of tAPX to the ROS scavenging, a tomato thylakoidal ascorbate peroxidase gene (LetAPX) was isolated and transgenic tomatoes were obtained. The LetAPX-GFP fusion protein was targeted to chloroplast in Arabidopsis mesophyll protoplast. RNA blotting analysis revealed that the LetAPX transcript expression was up-regulated by chilling, high light, exogenous salicylic acid (SA) and methyl viologen (MV). Over expression of LetAPX in tomatoes conferred tolerance to chilling stress by maintaining higher reduced glutathione (GSH) content, chlorophyll and APX activities compared with wild type (WT) plants. Furthermore, transgenic plants showed lower levels of hydrogen peroxide (H(2)O(2)) and ion leakage, lower malendialdehyde (MDA) content, higher net photosynthetic rate (Pn) and higher maximal photochemical efficiency of PSII (Fv/Fm). The oxidizable P700 decreased more obviously in WT than that in transgenic plants under chilling stress in low irradiance. The results suggested that over expression of tAPX played a key role both in alleviating photo inhibition of PSI and PSII and enhancing their tolerance to chilling stress.

title: Arabidopsis chloroplastic ascorbate peroxidase isoenzymes play a dual role in photoprotection and gene regulation under photooxidative stress.
abstract: Though two types of chloroplastic ascorbate peroxidase (APX) located in the thylakoid membrane (tAPX) and stroma (sAPX) have been thought to be key regulators of intracellular levels of H(2)O(2), their physiological significance in the response to photooxidative stress is still under discussion. Here we characterized single mutants lacking either tAPX (KO-tAPX) or sAPX (KO-sAPX). Under exposure to high light or treatment with methylviologen under light, H(2)O(2) and oxidized proteins accumulated to higher levels in both mutant plants than in the wild-type plants. On the other hand, the absence of sAPX and tAPX drastically suppressed the expression of H(2)O(2)-responsive genes under photooxidative stress. Interestingly, the most marked effect of photooxidative stress on the accumulation of H(2)O(2) and oxidized protein and gene expression was observed in the KO-tAPX plants rather than the KO-sAPX plants. The present findings suggest that both chloroplastic APXs, but particularly tAPX, are important for photoprotection and gene regulation under photooxidative stress in Arabidopsis leaves.

title: Impact of mitochondrial alternative oxidase expression on the response of Nicotiana tabacum to cold temperature.
abstract: The plant mitochondrial electron transport chain (ETC) includes a non-energy conserving alternative oxidase (AOX) thought to dampen reactive oxygen species (ROS) generation by the ETC and/or facilitate carbon metabolism by uncoupling it from ATP turnover. When wild-type (WT) Nicotiana tabacum grown at 28°C/22°C (light/dark) were transferred to 12°C/5°C, they showed a large induction of leaf Aox1a mRNA and AOX protein within 24 h. Transfer to cold also resulted in a large accumulation of monosaccharides, an increase in transcript level of genes encoding important ROS-scavenging enzymes and a moderate increase in lipid peroxidation. Transgenic plants with suppressed AOX level showed less cold-induced sugar accumulation than WT while transgenic plants with enhanced AOX levels showed enhanced sugar accumulation. This is inconsistent with the hypothesis that AOX acts to burn excess carbohydrate, but rather suggests a role for AOX to aid sugar accumulation, at least during cold stress. At 28°C/22°C, plants with suppressed AOX had elevated levels of lipid peroxidation compared with WT, while plants with enhanced AOX had reduced lipid peroxidation. This is consistent with the hypothesis that AOX dampens ROS generation and oxidative damage. However, this inverse relationship between AOX level and lipid peroxidation did not hold upon shift to cold. Under this stress condition, plants with strong suppression of AOX show enhanced induction of ROS-scavenging enzymes compared with WT and decline in lipid peroxidation. These data suggest that, under stress conditions, the lack of AOX enhances a mitochondrial stress-signaling pathway able to increase the ROS-scavenging capacity of the cell.

title: A single amino acid change in the plant alternative oxidase alters the specificity of organic acid activation
abstract: The alternative oxidase is a quinol oxidase of the respiratory chain of plants and some fungi and protists. Its activity is regulated by redox-sensitive disulphide bond formation between neighbouring subunits and direct interaction with certain alpha-ketoacids. To investigate these regulatory mechanisms, we undertook site-directed mutagenesis of soybean and Arabidopsis alternative oxidase cDNAs, and expressed them in tobacco plants and Escherichia coli, respectively. The homologous C99 and C127 residues of GmAOX3 and AtAOX1a, respectively, were changed to serine. In the plant system, this substitution prevented oxidative inactivation of alternative oxidase and rendered the protein insensitive to pyruvate activation, in agreement with the recent results from other laboratories [Rhoads et al. (1998) ; Vanlerberghe et al. (1998) ]. However, the mutated protein is instead activated specifically by succinate. Measurements of AtAOX1a activity in bacterial membranes lacking succinate dehydrogenase confirmed that the stimulation of the mutant protein's activity by succinate did not involve its metabolism. Examples of alternative oxidase proteins with the C to S substitution occur in nature and these oxidases are expected to be activated under most conditions in vivo, with implications for the efficiency of respiration in the tissues which express them.

title: Activation of the plant mitochondrial alternative oxidase: insights from site-directed mutagenesis.
abstract: The homodimeric cyanide-resistant alternative oxidase of plant mitochondria reduces oxygen to water without forming ATP. Arabidopsis thaliana alternative oxidase AOX1a is stimulated by pyruvate or other alpha-keto acids associating with a regulatory cysteine at position 78, by succinate in a serine-78 mutant, and by site-directed mutation of position 78 to glutamate. The mechanism of activation was explored with additional amino acid substitutions made at Cys-78 in AOX1a, which was functionally expressed in Escherichia coli. Oxidases with positively charged substitutions (Lys and Arg) were insensitive to pyruvate or succinate but were more active than the wild type without pyruvate. Uncharged substitutions (Gln, Leu) produced an inactive enzyme. These results indicate that activation may be due to conformational changes caused by charge repulsion between the dimer subunits and not through a direct role of alpha-keto acids in catalysis. Oxygen isotope fractionation experiments suggest that the charge of the amino acid at position 78 also affects the entry of oxygen into the active site. Therefore, the N-terminal portion of the protein containing residue 78 can indirectly affect both catalysis at the diiron active site and the path of oxygen to that site. In addition, both positively and negatively substituted alternative oxidases were stimulated by glyoxylate, suggesting the presence of a second activation site, possibly Cys-128.

title: Decreased Expression of Cytosolic Pyruvate Kinase in Potato Tubers Leads to a Decline in Pyruvate Resulting in an in Vivo Repression of the Alternative Oxidase1[W][OA]
abstract: The aim of this work was to investigate the effect of decreased cytosolic pyruvate kinase (PKc) on potato (Solanum tuberosum) tuber metabolism. Transgenic potato plants with strongly reduced levels of PKc were generated by RNA interference gene silencing under the control of a tuber-specific promoter. Metabolite profiling showed that decreased PKc activity led to a decrease in the levels of pyruvate and some other organic acids involved in the tricarboxylic acid cycle. Flux analysis showed that this was accompanied by changes in carbon partitioning, with carbon flux being diverted from glycolysis toward starch synthesis. However, this metabolic shift was relatively small and hence did not result in enhanced starch levels in the tubers. Although total respiration rates and the ATP to ADP ratio were largely unchanged, transgenic tubers showed a strong decrease in the levels of alternative oxidase (AOX) protein and a corresponding decrease in the capacity of the alternative pathway of respiration. External feeding of pyruvate to tuber tissue or isolated mitochondria resulted in activation of the AOX pathway, both in the wild type and the PKc transgenic lines, providing direct evidence for the regulation of AOX by changes in pyruvate levels. Overall, these results provide evidence for a crucial role of PKc in the regulation of pyruvate levels as well as the level of the AOX in heterotrophic plant tissue, and furthermore reveal that these parameters are interlinked in vivo.

title: Regulation of Respiration and Fermentation to Control the Plant Internal Oxygen Concentration1[OA]
abstract: Plant internal oxygen concentrations can drop well below ambient even when the plant grows under optimal conditions. Using pea (Pisum sativum) roots, we show how amenable respiration adapts to hypoxia to save oxygen when the oxygen availability decreases. The data cannot simply be explained by oxygen being limiting as substrate but indicate the existence of a regulatory mechanism, because the oxygen concentration at which the adaptive response is initiated is independent of the actual respiratory rate. Two phases can be discerned during the adaptive reaction: an initial linear decline of respiration is followed by a nonlinear inhibition in which the respiratory rate decreased progressively faster upon decreasing oxygen availability. In contrast to the cytochrome c pathway, the inhibition of the alternative oxidase pathway shows only the linear component of the adaptive response. Feeding pyruvate to the roots led to an increase of the oxygen consumption rate, which ultimately led to anoxia. The importance of balancing the in vivo pyruvate availability in the tissue was further investigated. Using various alcohol dehydrogenase knockout lines of Arabidopsis (Arabidopsis thaliana), it was shown that even under aerobic conditions, alcohol fermentation plays an important role in the control of the level of pyruvate in the tissue. Interestingly, alcohol fermentation appeared to be primarily induced by a drop in the energy status of the tissue rather than by a low oxygen concentration, indicating that sensing the energy status is an important component of optimizing plant metabolism to changes in the oxygen availability.

title: Purification, microsequencing and cloning of spinach ATP‐dependent phosphofructokinase link sequence and function for the plant enzyme
abstract: 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 ∼52 kDa subunits with a specific activity of 600 mU·mg−1 and a Km value for ATP of 81 µm. The purified enzyme was not activated by phosphate, but slightly inhibited instead, suggesting that it was the chloroplast isoform. The inclusion of adenosine 5′‐(β,γ‐imido)triphosphate was conducive to enzyme activitiy 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.

title: PHOSPHOENOLPYRUVATE CARBOXYLASE: A Ubiquitous, Highly Regulated Enzyme in Plants.
abstract: Since plant phosphoenolpyruvate carboxylase (PEPC) was last reviewed in the Annual Review of Plant Physiology over a decade ago (O'Leary 1982), significant advances have been made in our knowledge of this oligomeric, cytosolic enzyme. This review highlights this exciting progress in plant PEPC research by focusing on the three major areas of recent investigation: the enzymology of the protein; its posttranslational regulation by reversible protein phosphorylation and opposing metabolite effectors; and the structure, expression, and molecular evolution of the nuclear PEPC genes. It is hoped that the next ten years will be equally enlightening, especially with respect to the three-dimensional structure of the plant enzyme, the molecular analysis of its highly regulated protein-Ser/Thr kinase, and the elucidation of its associated signal-transduction pathways in various plant cell types.

title: Purification and characterization of phosphoenolpyruvate carboxylase from Brassica napus (rapeseed) suspension cell cultures: implications for phosphoenolpyruvate carboxylase regulation during phosphate starvation, and the integration of glycolysis with nitrogen assimilation.
abstract: Phosphoenolpyruvate carboxylase (PEPC) specific activity increased by 250% following 8 to 10 days of Pi starvation of Brassica napus suspension cells. Densitometric scanning of PEPC immunoblots revealed a close correlation between PEPC activity and the amount of the antigenic 104-kDa PEPC subunit. To further assess the influence of Pi deprivation on PEPC, the enzyme was purified from Pi-sufficient (+Pi) and Pi-starved (-Pi) cells to electrophoretic homogeneity and final specific activities of 37-40 micromol phosphoenolpyruvate utilized per min per mg protein. Gel filtration, SDS/PAGE, and CNBr peptide mapping indicated that the +Pi and -Pi PEPCs are both homotetramers composed of an identical 104-kDa subunit. Respective pH-activity profiles, phosphoenolpyruvate saturation kinetics, and sensitivity to L-malate inhibition were also indistinguishable. Kinetic studies and phosphatase treatments revealed that PEPC of the +Pi and -Pi cells exists mainly in its dephosphorylated (L-malate sensitive) form. Thus, up-regulation of PEPC activity in -Pi cells appears to be solely due to the accumulation of the same PEPC isoform being expressed in +Pi cells. PEPC activity was modulated by several metabolites involved in carbon and nitrogen metabolism. At pH 7.3, marked activation by glucose 6-phosphate and inhibition by L-malate, L-aspartate, L-glutamate, DL-isocitrate, rutin and quercetin was observed. The following paper provides a model for the coordinate regulation of B. napus PEPC and cytosolic pyruvate kinase by allosteric effectors. L-Aspartate and L-glutamate appear to play a crucial role in the control of the phosphoenolpyruvate branchpoint in B. napus, particularly with respect to the integration of carbohydrate partitioning with the generation of carbon skeletons required during nitrogen assimilation.

title: The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase): recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs.
abstract: PEPC [PEP (phosphoenolpyruvate) carboxylase] is a tightly controlled enzyme located at the core of plant C-metabolism that catalyses the irreversible β-carboxylation of PEP to form oxaloacetate and Pi. The critical role of PEPC in assimilating atmospheric CO(2) during C(4) and Crassulacean acid metabolism photosynthesis has been studied extensively. PEPC also fulfils a broad spectrum of non-photosynthetic functions, particularly the anaplerotic replenishment of tricarboxylic acid cycle intermediates consumed during biosynthesis and nitrogen assimilation. An impressive array of strategies has evolved to co-ordinate in vivo PEPC activity with cellular demands for C(4)-C(6) carboxylic acids. To achieve its diverse roles and complex regulation, PEPC belongs to a small multigene family encoding several closely related PTPCs (plant-type PEPCs), along with a distantly related BTPC (bacterial-type PEPC). PTPC genes encode ~110-kDa polypeptides containing conserved serine-phosphorylation and lysine-mono-ubiquitination sites, and typically exist as homotetrameric Class-1 PEPCs. In contrast, BTPC genes encode larger ~117-kDa polypeptides owing to a unique intrinsically disordered domain that mediates BTPC's tight interaction with co-expressed PTPC subunits. This association results in the formation of unusual ~900-kDa Class-2 PEPC hetero-octameric complexes that are desensitized to allosteric effectors. BTPC is a catalytic and regulatory subunit of Class-2 PEPC that is subject to multi-site regulatory phosphorylation in vivo. The interaction between divergent PEPC polypeptides within Class-2 PEPCs adds another layer of complexity to the evolution, physiological functions and metabolic control of this essential CO(2)-fixing plant enzyme. The present review summarizes exciting developments concerning the functions, post-translational controls and subcellular location of plant PTPC and BTPC isoenzymes.

title: From enzyme activity to plant biotechnology: 30 years of research on phosphoenolpyruvate carboxylase
abstract: This paper reviews the contribution of P. Gadal’s group to the study of phosphoenolpyruvate carboxylase (PEPC) in plants. It highlights how molecular biology and genetics have helped to advance our understanding of the PEPC multigene family, including evolutionary aspects, and the regulatory mechanisms controlling the expression of the gene encoding the photosynthetic isoform of C4 plants. Preliminary experiments using plant transformation with the aim of determining the role of PEPC isoforms in different physiological contexts and to improve crop yield are also reported.

title: Identification of a Novel Transporter for Dicarboxylates and Tricarboxylates in Plant Mitochondria
abstract: A cDNA from Arabidopsis thalianaand four related cDNAs from Nicotiana tabacum that we have isolated encode hitherto unidentified members of the mitochondrial carrier family. These proteins have been overexpressed in bacteria and reconstituted into phospholipid vesicles. Their transport properties demonstrate that they are orthologs/isoforms of a novel mitochondrial carrier capable of transporting both dicarboxylates (such as malate, oxaloacetate, oxoglutarate, and maleate) and tricarboxylates (such as citrate, isocitrate, cis-aconitate, andtrans-aconitate). The newly identified dicarboxylate-tricarboxylate carrier accepts only the single protonated form of citrate (H-citrate2−) and the unprotonated form of malate (malate2−) and catalyzes obligatory, electroneutral exchanges. Oxoglutarate, citrate, and malate are mutually competitive inhibitors, showing K i close to the respectiveK m . The carrier is expressed in all plant tissues examined and is largely spread in the plant kingdom. Furthermore, nitrate supply to nitrogen-starved tobacco plants leads to an increase in its mRNA in roots and leaves. The dicarboxylate-tricarboxylate carrier may play a role in important plant metabolic functions requiring organic acid flux to or from the mitochondria, such as nitrogen assimilation, export of reducing equivalents from the mitochondria, and fatty acid elongation.

title: Experimental Analysis of the Arabidopsis Mitochondrial Proteome Highlights Signaling and Regulatory Components, Provides Assessment of Targeting Prediction Programs, and Indicates Plant-Specific Mitochondrial Proteins Online version contains Web-only data. Article, publication date, and citation inf
abstract: A novel insight into Arabidopsis mitochondrial function was revealed from a large experimental proteome derived by liquid chromatography–tandem mass spectrometry. Within the experimental set of 416 identified proteins, a significant number of low-abundance proteins involved in DNA synthesis, transcriptional regulation, protein complex assembly, and cellular signaling were discovered. Nearly 20% of the experimentally identified proteins are of unknown function, suggesting a wealth of undiscovered mitochondrial functions in plants. Only approximately half of the experimental set is predicted to be mitochondrial by targeting prediction programs, allowing an assessment of the benefits and limitations of these programs in determining plant mitochondrial proteomes. Maps of putative orthology networks between yeast, human, and Arabidopsis mitochondrial proteomes and the Rickettsia prowazekii proteome provide detailed insights into the divergence of the plant mitochondrial proteome from those of other eukaryotes. These show a clear set of putative cross-species orthologs in the core metabolic functions of mitochondria, whereas considerable diversity exists in many signaling and regulatory functions.

title: Characterization of a mutation in the IDH-II subunit of the NAD+-dependent isocitrate dehydrogenase from Arabidopsis thaliana
abstract: The mitochondrial NAD+-dependent isocitrate dehydrogenase (EC 1.1.1.41) is a key enzyme in the Krebs cycle of most organisms. The role of the IDH-II subunit of this protein in Arabidopsis thaliana was investigated using an idh-II knockout mutant where the IDH-II gene was disrupted by the Dissociation, (Ds), insertion element. These mutant plants showed no detectable differences in growth and development compared to wildtype Landsberg plants. Mitochondria from the idh-II mutant had substantially less NAD+-isocitrate dehydrogenase activity when measured in vitro but this did not appear to alter rates of tissue respiration or photosynthesis. These results suggest that the other NAD+-isocitrate dehydrogenase subunits can substitute for the missing IDH-II protein and that NAD+-IDH activity does not limit whole plant respiration as suggested by the low in vitro activity of this enzyme.

title: Understanding fatty acid synthesis in developing maize embryos using metabolic flux analysis.
abstract: The efficiency with which developing maize embryos convert substrates into seed storage reserves was determined to be 57-71%, by incubating developing maize embryos with uniformly labeled 14C substrates and measuring their conversion to CO2 and biomass products. To map the pattern of metabolic fluxes underlying this efficiency, maize embryos were labeled to isotopic steady state using a combination of labeled 13C-substrates. Intermediary metabolic fluxes were estimated by computer-aided modeling of the central metabolic network using the labeling data collected by NMR and GC-MS and the biomass composition. The resultant flux map reveals that even though 36% of the entering carbon goes through the oxidative pentose-phosphate pathway, this does not fully meet the NADPH demands for fatty acid synthesis. Metabolic flux analysis and enzyme activities highlight the importance of plastidic NADP-dependent malic enzyme, which provides one-third of the carbon and NADPH required for fatty acid synthesis in developing maize embryos.

title: The role of light in soybean seed filling metabolism.
abstract: Soybean (Glycine max) yields high levels of both protein and oil, making it one of the most versatile and important crops in the world. Light has been implicated in the physiology of developing green seeds including soybeans but its roles are not quantitatively understood. We have determined the light levels reaching growing soybean embryos under field conditions and report detailed redox and energy balance analyses for them. Direct flux measurements and labeling patterns for multiple labeling experiments including [U-(13)C(6)]-glucose, [U-(13)C(5)]-glutamine, the combination of [U-(14)C(12)]-sucrose + [U-(14)C(6)]-glucose + [U-(14)C(5)]-glutamine + [U-(14)C(4)]-asparagine, or (14)CO2 labeling were performed at different light levels to give further insight into green embryo metabolism during seed filling and to develop and validate a flux map. Labeling patterns (protein amino acids, triacylglycerol fatty acids, starch, cell wall, protein glycan monomers, organic acids), uptake fluxes (glutamine, asparagine, sucrose, glucose), fluxes to biomass (protein amino acids, oil), and respiratory fluxes (CO2, O2) were established by a combination of gas chromatography-mass spectrometry, (13)C- and (1)H-NMR, scintillation counting, HPLC, gas chromatography-flame ionization detection, C:N and amino acid analyses, and infrared gas analysis, yielding over 750 measurements of metabolism. Our results show: (i) that developing soybeans receive low but significant light levels that influence growth and metabolism; (ii) a role for light in generating ATP but not net reductant during seed filling; (iii) that flux through Rubisco contributes to carbon conversion efficiency through generation of 3-phosphoglycerate; and (iv) a larger contribution of amino acid carbon to fatty acid synthesis than in other oilseeds analyzed to date.

title: Metabolic flux analysis in plants: coping with complexity.
abstract: Theory and experience in metabolic engineering both show that metabolism operates at the network level. In plants, this complexity is compounded by a high degree of compartmentation and the synthesis of a very wide array of secondary metabolic products. A further challenge to understanding and predicting plant metabolic function is posed by our ignorance about the structure of metabolic networks even in well-studied systems. Metabolic flux analysis (MFA) provides tools to measure and model the functioning of metabolism, and is making significant contributions to coping with their complexity. This review gives an overview of different MFA approaches, the measurements required to implement them and the information they yield. The application of MFA methods to plant systems is then illustrated by several examples from the recent literature. Next, the challenges that plant metabolism poses for MFA are discussed together with ways that these can be addressed. Lastly, new developments in MFA are described that can be expected to improve the range and reliability of plant MFA in the coming years.

title: Parallel determination of enzyme activities and in vivo fluxes in Brassica napus embryos grown on organic or inorganic nitrogen source.
abstract: After the completion of the genomic sequencing of model organisms, numerous post-genomic studies, integrating transcriptome and metabolome data, are aimed at developing a more complete understanding of cell physiology. Here, we measure in vivo metabolic fluxes by steady state labeling, and in parallel, the activity of enzymes in central metabolism in cultured developing embryos of Brassica napus. Embryos were grown on either the amino acids glutamine and alanine as an organic nitrogen source, or on ammonium nitrate as an inorganic nitrogen source. The type of nitrogen made available to developing embryos caused substantial differences in fluxes associated with the tricarboxylic acid cycle, including flux reversion. The changes observed in enzyme activity were not consistent with our estimates of metabolic flux. Furthermore, most extractable enzyme activities are in large surplus relative to the requirements for the observed in vivo fluxes. The results demonstrate that in this model system the metabolic response of central metabolism to changes in environmental conditions can be achieved largely without regulatory reprogramming of the enzyme machinery.

title: Analysis of Metabolic Flux Phenotypes for Two Arabidopsis Mutants with Severe Impairment in Seed Storage Lipid Synthesis1[W][OA]
abstract: Major storage reserves of Arabidopsis (Arabidopsis thaliana) seeds are triacylglycerols (seed oils) and proteins. Seed oil content is severely reduced for the regulatory mutant wrinkled1 (wri1-1; At3g54320) and for a double mutant in two isoforms of plastidic pyruvate kinase (pkpβ1pkpα; At5g52920 and At3g22960). Both already biochemically well-characterized mutants were now studied by 13C metabolic flux analysis of cultured developing embryos based on comparison with their respective genetic wild-type backgrounds. For both mutations, in seeds as well as in cultured embryos, the oil fraction was strongly reduced while the fractions of proteins and free metabolites increased. Flux analysis in cultured embryos revealed changes in nutrient uptakes and fluxes into biomass as well as an increase in tricarboxylic acid cycle activity for both mutations. While in both wild types plastidic pyruvate kinase (PKp) provides most of the pyruvate for plastidic fatty acid synthesis, the flux through PKp is reduced in pkpβ1pkpα by 43% of the wild-type value. In wri1-1, PKp flux is even more reduced (by 82%), although the genes PKpβ1 and PKpα are still expressed. Along a common paradigm of metabolic control theory, it is hypothesized that a large reduction in PKp enzyme activity in pkpβ1pkpα has less effect on PKp flux than multiple smaller reductions in glycolytic enzymes in wri1-1. In addition, only in the wri1-1 mutant is the large reduction in PKp flux compensated in part by an increased import of cytosolic pyruvate and by plastidic malic enzyme. No such limited compensatory bypass could be observed in pkpβ1pkpα.

title: Metabolic flux maps comparing the effect of temperature on protein and oil biosynthesis in developing soybean cotyledons.
abstract: Metabolic flux maps developed from 13C metabolic flux analysis (13C MFA) are effective tools for assessing the response of biological systems to genetic or environmental perturbations, and for identifying possible metabolic engineering targets. Experimental treatments were designed to distinguish between temperature effects prior to, and during incubation in vitro, on primary metabolism in developing soybeans. Biomass accumulation increased with temperature as did carbon partitioning into lipids. The flux through the plastidic oxidative pentose phosphate pathway (pgl(P)) relative to sucrose intake remained fairly constant [ approximately 56% (+/-24%)] when cotyledons were transferred from an optimum growth temperature to varying temperatures in in vitro culture, signifying a rigid node under these conditions. However, pgl(P) flux ranged from 57 to 77% of sucrose intake when growth temperature in planta varied and were cultured in vitro at the same temperature (as the plant), indicating a flexible node for this case. The carbon flux through the anaplerotic reactions catalysed by plastidic malic enzyme (me(P)), cytosolic phosphoenolpyruvate (PEP) carboxylase and the malate (Mal) transporter from the cytosol to mitochondrion varied dramatically with temperature and had a direct influence on the carbon partitioning into protein and oil from the plastidic pyruvate (Pyr) pool. These results of the in vitro culture indicate that temperature during early stages of development has a dominant effect on establishing capacity for flux through certain components of central carbon metabolism.

title: Identification of hexose hydrolysis products in metabolic flux analytes: a case study of levulinic acid in plant protein hydrolysate.
abstract: Biosynthetically directed fractional (13)C labeling, a popular methodology of metabolic flux analysis, involves culture on a mixture of (13)C and (12)C substrates and preparation a 'metabolic flux analyte' (typically protein hydrolysate) from the biomass. Metabolic flux analytes prepared from complex eukaryotes may contain additional compounds than those prepared from microorganisms. We report the presence of such compounds (hexose hydrolysis products) in a plant metabolic flux analyte (acid hydrolyzed protein from soybean embryos). We designed NMR experiments to systematically identify these compounds, and found that they were levulinic acid (LVA; major) and hydroxyacetone (HyA; minor). These acid hydrolysis products of hexoses (glucose and mannose) were generated during acid hydrolysis of glycosylating sugars (glucosamine and mannose) associated with soybean embryo protein. Analysis of LVA by two-dimensional [(13)C, (1)H] NMR and measurement of its J-coupling constants revealed long-range coupling between atoms C3 and C5, which enables LVA to provide more isotopomer information than its precursor hexose. Furthermore, we found that LVA and HyA preserve the isotopomeric composition of the metabolic hexose from which they are derived. An important consequence of these results is that comparison of LVA and HyA isotopomers from two separate metabolic flux analytes (protein hydrolysate and starch hydrolysate) from the same plant tissue can distinguish between parallel glycolysis and pentose phosphate pathways in different subcellular compartments.

title: Metabolic dynamics during autumn cold acclimation within and among populations of Sitka spruce (Picea sitchensis).
abstract: Autumnal cold acclimation in conifers is a complex process, the timing and extent of which vary widely along latitudinal gradients for many tree species and reflect local adaptation to climate. Although previous studies have detailed some aspects of the metabolic remodelling that accompanies cold acclimation in conifers, little is known about global metabolic dynamics, or how these changes vary among phenotypically divergent populations. • Using untargeted GC-MS metabolite profiling, we monitored metabolic dynamics during autumnal cold acclimation in three populations of Sitka spruce from the southern, central, and northern portions of the species range, which differ in both the timing and extent of cold acclimation. • Latitudinal variation was evident in the nature, intensity, and timing of metabolic events. Early development of strong freezing tolerance in the northern population was associated with a transient accumulation of amino acids. By late autumn, metabolic profiles were highly similar between the northern and central populations, whereas profiles for the southern population were relatively distinct. • Our results provide insight into the metabolic architecture of latitudinal adaptive variation in autumn acclimation and show that different mechanisms are the basis of early October cold hardiness and autumn-acclimated cold hardiness.

title: Differential fumarate binding to Arabidopsis NAD+-malic enzymes 1 and -2 produces an opposite activity modulation.
abstract: Arabidopsis mitochondria contain two NAD(+)-malic enzymes, NAD-ME1 and NAD-ME2. These proteins have similar affinity for their substrates but display opposite regulation by fumarate, which strongly stimulates NAD-ME1 but inhibits NAD-ME2 activity. Here, the interaction of NAD-ME1 and -2 with fumarate was investigated by kinetic approaches, urea denaturation assays and intrinsic fluorescence quenching, in the absence and presence of NAD(+). Fumarate inhibited NAD-ME2 at saturating, but not at low, levels of NAD(+), and it behaved as competitive inhibitor with respect to L-malate. In contrast, NAD-ME1 fumarate activation was higher at suboptimal NAD(+) concentrations. In the absence of cofactor, the fluorescence of both NAD-ME1 and -2 is quenched by fumarate. However, for NAD-ME2 the quenching arises from a collisional phenomenon, while in NAD-ME1 the fluorescence decay can be explained by a static process that involves fumarate binding to the protein. Furthermore, the residue Arg84 of NAD-ME1 is essential for fumarate binding, as the mutant protein R84A exhibits a collisional quenching by this metabolite. Together, the results indicate that the differential fumarate regulation of Arabidopsis NAD-MEs, which is further modulated by NAD(+) availability, is related to the gaining of an allosteric site for fumarate in NAD-ME1 and an active site-associated inhibition by this C(4)-organic acid in NAD-ME2.

title: A Bypass of Sucrose Synthase Leads to Low Internal Oxygen and Impaired Metabolic Performance in Growing Potato Tubers1
abstract: Plants possess two alternative biochemical pathways for sucrose (Suc) degradation. One involves hydrolysis by invertase followed by phosphorylation via hexokinase and fructokinase, and the other route—which is unique to plants—involves a UDP-dependent cleavage of Suc that is catalyzed by Suc synthase (SuSy). In the present work, we tested directly whether a bypass of the endogenous SuSy route by ectopic overexpression of invertase or Suc phosphorylase affects internal oxygen levels in growing tubers and whether this is responsible for their decreased starch content. (a) Oxygen tensions were lower within transgenic tubers than in wild-type tubers. Oxygen tensions decreased within the first 10 mm of tuber tissue, and this gradient was steeper in transgenic tubers. (b) Invertase-overexpressing tubers had higher activities of glyceraldehyde-3-phosphate dehydrogenase, lactate dehydrogenase, and alcohol dehydrogenase, and (c) higher levels of lactate. (d) Expression of a low-oxygen-sensitive Adh1-β-glucuronidase reporter gene construct was more strongly induced in the invertase-overexpressing background compared with wild-type background.  Intact transgenic tubers had lower ATP to ADP ratios than the wild type. ATP to ADP ratio was restored to wild type, when discs of transgenic tubers were incubated at 21% (v/v) oxygen. (f) Starch decreased from the periphery to the center of the tuber. This decrease was much steeper in the transgenic lines, leading to lower starch content especially near the center of the tuber. (g) Metabolic fluxes (based on redistribution of 14C-glucose) and ATP to ADP ratios were analyzed in more detail, comparing discs incubated at various external oxygen tensions (0%, 1%, 4%, 8%, 12%, and 21% [v/v]) with intact tubers. Discs of Suc phosphorylase-expressing lines had similar ATP to ADP ratios and made starch as fast as wild type in high oxygen but had lower ATP to ADP ratios and lower rates of starch synthesis than wild type at low-oxygen tensions typical to those found inside an intact tuber. (h) In discs of wild-type tubers, subambient oxygen concentrations led to a selective increase in the mRNA levels of specific SuSy genes, whereas the mRNA levels of genes encoding vacuolar and apoplastic invertases decreased. (i) These results imply that repression of invertase and mobilization of Suc via the energetically less costly route provided by SuSy is important in growing tubers because it conserves oxygen and allows higher internal oxygen tensions to be maintained than would otherwise be possible.

title: Regulation of Starch Biosynthesis in Response to a Fluctuating Environment1
abstract: Starch is the major storage carbohydrate in higher plants, with many important functions. In photosynthesizing leaves, starch accumulates during the day and is remobilized at night to support continued respiration, Suc export, and growth in the dark ([Geiger and Servaites, 1994][1]). In this context

title: Progress in Arabidopsis starch research and potential biotechnological applications.
abstract: For the past decade, Arabidopsis has been the model higher plant of choice. Research into leaf starch metabolism has demonstrated that Arabidopsis is a useful system in which to make fundamental discoveries about both starch biosynthesis and starch degradation. This review describes recent discoveries in these fields and illustrates how such discoveries might be applied in the green biotechnology sector to improve and diversify our starch crops.

title: Starch biosynthesis in cereal endosperm.
abstract: Stored starch generally consists of two d-glucose homopolymers, the linear polymer amylose and a highly branched glucan amylopectin that connects linear chains. Amylopectin structurally contributes to the crystalline organization of the starch granule in cereals. In the endosperm, amylopectin biosynthesis requires the proper execution of a coordinated series of enzymatic reactions involving ADP glucose pyrophosphorylase (AGPase), soluble starch synthase (SS), starch branching enzyme (BE), and starch debranching enzyme (DBE), whereas amylose is synthesized by AGPase and granule-bound starch synthase (GBSS). It is highly possible that plastidial starch phosphorylase (Pho1) plays an important role in the formation of primers for starch biosynthesis in the endosperm. Recent advances in our understanding of the functions of individual enzyme isoforms have provided new insights into how linear polymer chains and branch linkages are synthesized in cereals. In particular, genetic analyses of a suite of mutants have formed the basis of a new model outlining the role of various enzyme isoforms in cereal starch production. In our current review, we summarize the recent research findings related to starch biosynthesis in cereal endosperm, with a particular focus on rice.

title: Regulation of starch metabolism: the age of enlightenment?
abstract: Starch and sucrose are the primary products of photosynthesis in the leaves of most plants. Starch represents the major plant storage carbohydrate providing energy during the times of heterotrophic growth. Starch metabolism has been studied extensively, leading to a good knowledge of the numerous enzymes involved. In contrast, understanding of the regulation of starch metabolism is fragmentary. This review summarises briefly the known steps in starch metabolism, highlighting recent discoveries. We also focus on evidence for potential regulatory mechanisms of the enzymes involved. These mechanisms include allosteric regulation by metabolites, redox regulation, protein-protein interactions and reversible protein phosphorylation. Modern systems biology and bioinformatic approaches are uncovering evidence for extensive post-translational protein modifications that may underlie enzyme regulation and identify novel proteins which may be involved in starch metabolism.

title: Arabidopsis and primary photosynthetic metabolism - more than the icing on the cake.
abstract: Historically speaking, Arabidopsis was not the plant of choice for investigating photosynthesis, with physiologists and biochemists favouring other species such as Chlorella, spinach and pea. However, its inherent advantages for forward genetics rapidly led to its adoption for photosynthesis research. In the last ten years, the availability of the Arabidopsis genome sequence - still the gold-standard for plant genomes - and the rapid expansion of genetic and genomic resources have further increased its importance. Research in Arabidopsis has not only provided comprehensive information about the enzymes and other proteins involved in photosynthesis, but has also allowed transcriptional responses, protein levels and compartmentation to be analysed at a global level for the first time. Emerging technical and theoretical advances offer another leap forward in our understanding of post-translational regulation and the control of metabolism. To illustrate the impact of Arabidopsis, we provide a historical review of research in primary photosynthetic metabolism, highlighting the role of Arabidopsis in elucidation of the pathway of photorespiration and the regulation of RubisCO, as well as elucidation of the pathways of starch turnover and studies of the significance of starch for plant growth.

title: Coordination of carbon supply and plant growth.
abstract: Plants must achieve a balance between carbon assimilation, storage and growth, but little is known about how this is achieved. We describe evidence for the existence of regulatory mechanisms that coordinate carbon supply and use, and the likely central role of sugar signalling. We propose the existence of both 'acute' and 'acclimatory' responses to alterations in carbon supply, the latter tuning the balance between carbon supply and demand to optimise the capacity for sustained growth. A full understanding of these responses requires new, systems-level approaches that integrate information from transcriptomic, enzyme activity, metabolomic and growth analyses. We illustrate the complexity of acute and acclimatory responses by consideration of the control of starch synthesis and degradation in leaves. Finally, we consider how carbon balance may be linked to growth, and the importance of these linkages for sustained plant growth in a changing environment.

title: Food reserves of Scots pine (Pinus sylvestris L.)
abstract: SummaryThe amounts of starch, soluble sugars, triacylglycerols, diacylglycerols and free fatty acids were studied in Scots pine (Pinus sylvestris L.) during an annual cycle in current-year needles and in 1-, 2- and 3-year-old needles collected shortly after bud break. Determination of the compounds was performed using specific enzymatic assays, capillary gas chromatography and thin layer chromatography. Newly emerging needles contained relatively large amounts of starch, but only trace amounts of fat. During autumn and winter, fat content rose, while starch content decreased; amounts of both these reserve materials were very high the next spring shortly before bud break and decreased again during shoot elongation. Concentration of intermediates in triacylglycerol biosynthesis (diacylglycerols and free fatty acids), were low in summer and high in winter. The same pattern was observed for fructose and glucose (the predominant soluble sugars), galactose/arabinose and raffinose/melibiose. In contrast, sucrose concentrations were highest in spring and in autumn. Mature needles of different ages collected in May showed significant differences only in their triacylglycerol and starch content. Concentration changes of reserve materials are discussed in relation to season, mobilization and translocation processes, dormancy, frost resistance and the possibility of carbohydrate-fat interconversions.

title: Developmental Stage Specificity and the Role of Mitochondrial Metabolism in the Response of Arabidopsis Leaves to Prolonged Mild Osmotic Stress1[C][W][OA]
abstract: When subjected to stress, plants reprogram their growth by largely unknown mechanisms. To provide insights into this process, the growth of Arabidopsis (Arabidopsis thaliana) leaves that develop under mild osmotic stress was studied. Early during leaf development, cell number and size were reduced by stress, but growth was remarkably adaptable, as division and expansion rates were identical to controls within a few days of leaf initiation. To investigate the molecular basis of the observed adaptability, leaves with only proliferating, exclusively expanding, and mature cells were analyzed by transcriptomics and targeted metabolomics. The stress response measured in growing and mature leaves was largely distinct; several hundred transcripts and multiple metabolites responded exclusively in the proliferating and/or expanding leaves. Only a few genes were differentially expressed across the three stages. Data analysis showed that proliferation and expansion were regulated by common regulatory circuits, involving ethylene and gibberellins but not abscisic acid. The role of ethylene was supported by the analysis of ethylene-insensitive mutants. Exclusively in proliferating cells, stress induced genes of the so-called “mitochondrial dysfunction regulon,” comprising alternative oxidase. Up-regulation for eight of these genes was confirmed with promoter:β-glucuronidase reporter lines. Furthermore, mitochondria of stress-treated dividing cells were morphologically distinct from control ones, and growth of plants overexpressing the alternative oxidase gene was more tolerant to osmotic and drought stresses. Taken together, our data underline the value of analyzing stress responses in development and demonstrate the importance of mitochondrial respiration for sustaining cell proliferation under osmotic stress conditions.

title: A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize.
abstract: MapMan is a software tool that supports the visualization of profiling data sets in the context of existing knowledge. Scavenger modules generate hierarchical and essentially non-redundant gene ontologies ('mapping files'). An ImageAnnotator module visualizes the data on a gene-by-gene basis on schematic diagrams ('maps') of biological processes. The PageMan module uses the same ontologies to statistically evaluate responses at the pathway or processes level. The generic structure of MapMan also allows it to be used for transcripts, proteins, enzymes and metabolites. MapMan was developed for use with Arabidopsis, but has already been extended for use with several other species. These tools are available as downloadable and web-based versions. After providing an introduction to the scope and use of MapMan, we present a case study where MapMan is used to analyse the transcriptional response of the crop plant maize to diurnal changes and an extension of the night. We then explain how MapMan can be customized to visually and systematically compare responses in maize and Arabidopsis. These analyses illustrate how MapMan can be used to analyse and compare global transcriptional responses between phylogenetically distant species, and show that analyses at the level of functional categories are especially useful in cross-species comparisons.

title: The Systems Biology Graphical Notation
abstract: Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.

title: Cytoscape: a software environment for integrated models of biomolecular interaction networks.
abstract: networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

title: GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop
abstract: The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses over 800 networks from six organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data.  The GeneMANIA Cytoscape plugin is implemented in Java and is freely available at http://www.genemania.org/plugin/. Contact: gary.bader@utoronto.ca; quaid.morris@utoronto.ca

title: Mosaic: making biological sense of complex networks
abstract: We present a Cytoscape plugin called Mosaic to support interactive network annotation, partitioning, layout and coloring based on gene ontology or other relevant annotations.  Mosaic is distributed for free under the Apache v2.0 open source license and can be downloaded via the Cytoscape plugin manager. A detailed user manual is available on the Mosaic web site (http://nrnb.org/tools/mosaic).  apico@gladstone.ucsf.edu

title: A Predicted Interactome for Arabidopsis1[C][W][OA]
abstract: The complex cellular functions of an organism frequently rely on physical interactions between proteins. A map of all protein-protein interactions, an interactome, is thus an invaluable tool. We present an interactome for Arabidopsis (Arabidopsis thaliana) predicted from interacting orthologs in yeast (Saccharomyces cerevisiae), nematode worm (Caenorhabditis elegans), fruitfly (Drosophila melanogaster), and human (Homo sapiens). As an internal quality control, a confidence value was generated based on the amount of supporting evidence for each interaction. A total of 1,159 high confidence, 5,913 medium confidence, and 12,907 low confidence interactions were identified for 3,617 conserved Arabidopsis proteins. There was significant coexpression of genes whose proteins were predicted to interact, even among low confidence interactions. Interacting proteins were also significantly more likely to be found within the same subcellular location, and significantly less likely to be found in conflicting localizations than randomly paired proteins. A notable exception was that proteins located in the Golgi were more likely to interact with Golgi, vacuolar, or endoplasmic reticulum sorted proteins, indicating possible docking or trafficking interactions. These predictions can aid researchers by extending known complexes and pathways with candidate proteins. In addition we have predicted interactions for many previously unknown proteins in known pathways and complexes. We present this interactome, and an online Web interface the Arabidopsis Interactions Viewer, as a first step toward understanding global signaling in Arabidopsis, and to whet the appetite for those who are awaiting results from high-throughput experimental approaches.