The presequence of Arabidopsis serine hydroxymethyltransferase SHM2 selectively prevents import into mesophyll mitochondria

CsSHMT3 gene enhances the growth and development in cucumber seedlings under salt stress

Salt stress is one of the major factors limiting plant growth and productivity. Many studies have shown that serine hydroxymethyltransferase (SHMT) gene play an important role in growth, development and stress response in plants. However, to date, there have been few studies on whether SHMT3 can enhance salt tolerance in plants. Therefore, the effects of overexpression or silencing of CsSHMT3 gene on cucumber seedling growth under salt stress were investigated in this study. The results showed that overexpression of CsSHMT3 gene in cucumber seedlings resulted in a significant increase in chlorophyll content, photosynthetic rate and proline (Pro) content, and antioxidant enzyme activity under salt stress condition; whereas the content of malondialdehyde (MDA), superoxide anion (H2O2), hydrogen peroxide (O2·-) and relative conductivity were significantly decreased when CsSHMT3 gene was overexpressed. However, the content of chlorophyll and Pro, photosynthetic rate, and antioxidant enzyme activity of the silenced CsSHMT3 gene lines under salt stress were significantly reduced, while MDA, H2O2, O2·- content and relative conductivity showed higher level in the silenced CsSHMT3 gene lines. It was further found that the expression of stress-related genes SOD, CAT, SOS1, SOS2, NHX, and HKT was significantly up-regulated by overexpressing CsSHMT3 gene in cucumber seedlings; while stress-related gene expression showed significant decrease in silenced CsSHMT3 gene seedlings under salt stress. This suggests that overexpression of CsSHMT3 gene increased the salt tolerance of cucumber seedlings, while silencing of CsSHMT3 gene decreased the salt tolerance. In conclusion, CsSHMT3 gene might positively regulate salt stress tolerance in cucumber and be involved in regulating antioxidant activity, osmotic adjustment, and photosynthesis under salt stress. KEY MESSAGE: CsSHMT3 gene may positively regulate the expression of osmotic system, photosynthesis, antioxidant system and stress-related genes in cucumber.

The serine-glycine-one-carbon metabolic network orchestrates changes in nitrogen and sulfur metabolism and shapes plant development

L-serine (Ser) and L-glycine (Gly) are critically important for the overall functioning of primary metabolism. We investigated the interaction of the phosphorylated pathway of Ser biosynthesis (PPSB) with the photorespiration-associated glycolate pathway of Ser biosynthesis (GPSB) using Arabidopsis thaliana PPSB-deficient lines, GPSB-deficient mutants, and crosses of PPSB with GPSB mutants. PPSB-deficient lines mainly showed retarded primary root growth. Mutation of the photorespiratory enzyme Ser-hydroxymethyltransferase 1 (SHMT1) in a PPSB-deficient background resumed primary root growth and induced a change in the plant metabolic pattern between roots and shoots. Grafting experiments demonstrated that metabolic changes in shoots were responsible for the changes in double mutant development. PPSB disruption led to a reduction in nitrogen (N) and sulfur (S) contents in shoots and a general transcriptional response to nutrient deficiency. Disruption of SHMT1 boosted the Gly flux out of the photorespiratory cycle, which increased the levels of the one-carbon (1C) metabolite 5,10-methylene-tetrahydrofolate and S-adenosylmethionine. Furthermore, disrupting SHMT1 reverted the transcriptional response to N and S deprivation and increased N and S contents in shoots of PPSB-deficient lines. Our work provides genetic evidence of the biological relevance of the Ser-Gly-1C metabolic network in N and S metabolism and in interorgan metabolic homeostasis.

Harnessing enzyme cofactors and plant metabolism: an essential partnership

Cofactors are fundamental to the catalytic activity of enzymes. Additionally, because plants are a critical source of several cofactors (i.e., including their vitamin precursors) within the context of human nutrition, there have been several studies aiming to understand the metabolism of coenzymes and vitamins in plants in detail. For example, compelling evidence has been brought forth regarding the role of cofactors in plants; specifically, it is becoming increasingly clear that an adequate supply of cofactors in plants directly affects their development, metabolism, and stress responses. Here, we review the state-of-the-art knowledge on the significance of coenzymes and their precursors with regard to general plant physiology and discuss the emerging functions attributed to them. Furthermore, we discuss how our understanding of the complex relationship between cofactors and plant metabolism can be used for crop improvement.

Photorespiration - Rubisco's repair crew

The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O₂ as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO₂ fixation in the Calvin cycle. However, the CO₂-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO₂ and can also use O₂ in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO₂. This disadvantageous feature can be suppressed by CO₂-concentrating mechanisms, such as those that evolved in C₄ plants thirty million years ago, which enhance CO₂ fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C₄ plants, C₃-C₄ intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.

Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration

The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential (Y p ) of crops is vital to address these challenges. In this review, we explore a component ofY p that has yet to be optimised - that being improvements in the efficiency with which light energy is converted into biomass (ε c ) via modifications to CO2 fixed per unit quantum of light (α), efficiency of respiratory ATP production (ε prod ) and efficiency of ATP use (ε use ). For α, targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential forε prod to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improveε use via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high-throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step-change in yield potential of globally important crops.

Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives

Serine hydroxymethyltransferase (SHM) is one of the hallmarks of one-carbon metabolism. In plants, isoforms of SHM participate in photorespiration and/or transfer the one-carbon unit from L-serine to tetrahydrofolate (THF), hence producing 5,10-CH2-THF that is needed, e.g., for biosynthesis of methionine, thymidylate, and purines. These links highlight the importance of SHM activity in DNA biogenesis, its epigenetic methylations, and in stress responses. Plant genomes encode several SHM isoforms that localize to cytosol, mitochondria, plastids, and nucleus. In this work, we present a thorough functional and structural characterization of all seven SHM isoforms from Arabidopsis thaliana (AtSHM1-7). In particular, we analyzed tissue-specific expression profiles of the AtSHM genes. We also compared catalytic properties of the active AtSHM1-4 in terms of catalytic efficiency in both directions and inhibition by the THF substrate. Despite numerous attempts to rescue the SHM activity of AtSHM5-7, we failed, which points towards different physiological functions of these isoforms. Comparative analysis of experimental and predicted three-dimensional structures of AtSHM1-7 proteins indicated differences in regions that surround the entrance to the active site cavity.

Genome-Wide Analysis of Serine Hydroxymethyltransferase Genes in Triticeae Species Reveals That TaSHMT3A-1 Regulates Fusarium Head Blight Resistance in Wheat

Serine hydroxymethyltransferase (SHMT) plays a pivotal role in cellular one-carbon, photorespiration pathways and it influences the resistance to biotic and abiotic stresses. However, the function of SHMT proteins in wheat remains largely unexplored. In the present study, SHMT genes in five Triticeae species, Oryza sativa, and four dicotyledon species were identified based on whole genome information. The origin history of the target gene was traced by micro-collinearity analysis. Gene expression patterns of TaSHMTs in different tissues, various biotic stresses, exogenous hormones, and two biotic stresses were determined by Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). The function of the selected TaSHMT3A-1 was studied by barley stripe mosaic virus-induced gene silencing in common wheat Bainong207. A total of 64 SHMT members were identified and further classified into two main classes based on the structure of SHMT proteins. The gene structure and motif composition analyses revealed that SHMTs kept relatively conserved within the same subclasses. Interestingly, there was a gene, TdSHMT7B-1, on chromosome 7B of Triticum dicoccoides, but there was no SHMT gene on chromosome 7 of other analyzed Triticeae species; TdSHMT7B-1 had fewer exons and conserved motifs than the genes in the same subclass, suggesting that the gene of TdSHMT7B-1 has a notable evolutionary progress. The micro-collinearity relationship showed that no homologs of TaSHMT3A-1 and its two neighboring genes were found in the collinearity region of Triticum urartu, and there were 27 genes inserted into the collinearity region of T. urartu. Furthermore, qRT-PCR results showed that TaSHMT3A-1 was responsive to abiotic stresses (NaCl and cold), abscisic acid, methyl jasmonate, and hydrogen peroxide. Significantly, upon Fusarium graminearum infection, the expression of TaSHMT3A-1 was highly upregulated in resistant cultivar Sumai3. More importantly, silencing of TaSHMT3A-1 compromises Fusarium head blight resistance in common wheat Bainong207. Our new findings suggest that the TaSHMT3A-1 gene in wheat plays an important role in resistance to Fusarium head blight. This provides a valuable reference for further study on the function of this gene family.

Serine hydroxymethyltransferase participates in the synthesis of cysteine-rich storage proteins in rice seed

The low level of cysteine-rich proteins (lcrp) mutation indicates a decrease in cysteine-rich (CysR) prolamines, α-globulin, and glutelin. To identify the causing factor of lcrp mutation, to elucidate its function, and to elucidate the role of CysR proteins in the formation of protein bodies (PBs), lcrp mutant was analyzed. A linkage map of the LCRP gene was constructed and genomic DNA sequencing of a predicted gene within the mapped region demonstrated that LCRP encodes a serine hydroxymethyltransferase, which participates in glycine-serine interconversion of one-carbon metabolism in the sulfur assimilation pathway. The levels of l-Ser, Gly, and Met in the sulfur assimilation pathway in the lcrp seeds increased significantly compared to that in the wildtype (WT). As the lcrp mutation influences the growth of shoot and root, the effects of the addition to the medium of amino acids and other compounds on the sulfur assimilation pathway were studied. Electron-lucent PBs surrounded by ribosome-attached membranes were observed accumulating cysteine-poor prolamines in the lcrp seeds. Additionally, glutelin-containing PBs were smaller and distorted in the lcrp seeds compared to those in the WT. These analyses of PBs in the lcrp seeds suggest that cysteine-rich proteins play an important role in the formation of PBs in rice.

The phosphorylated pathway of serine biosynthesis links plant growth with nitrogen metabolism

Because it is the precursor for various essential cellular components, the amino acid serine is indispensable for every living organism. In plants, serine is synthesized by two major pathways: photorespiration and the phosphorylated pathway of serine biosynthesis (PPSB). However, the importance of these pathways in providing serine for plant development is not fully understood. In this study, we examine the relative contributions of photorespiration and PPSB to providing serine for growth and metabolism in the C3 model plant Arabidopsis thaliana. Our analyses of cell proliferation and elongation reveal that PPSB-derived serine is indispensable for plant growth and its loss cannot be compensated by photorespiratory serine biosynthesis. Using isotope labeling, we show that PPSB-deficiency impairs the synthesis of proteins and purine nucleotides in plants. Furthermore, deficiency in PPSB-mediated serine biosynthesis leads to a strong accumulation of metabolites related to nitrogen metabolism. This result corroborates 15N-isotope labeling in which we observed an increased enrichment in labeled amino acids in PPSB-deficient plants. Expression studies indicate that elevated ammonium uptake and higher glutamine synthetase/glutamine oxoglutarate aminotransferase (GS/GOGAT) activity causes this phenotype. Metabolic analyses further show that elevated nitrogen assimilation and reduced amino acid turnover into proteins and nucleotides are the most likely driving forces for changes in respiratory metabolism and amino acid catabolism in PPSB-deficient plants. Accordingly, we conclude that even though photorespiration generates high amounts of serine in plants, PPSB-derived serine is more important for plant growth and its deficiency triggers the induction of nitrogen assimilation, most likely as an amino acid starvation response.

Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses

The metabolism of an organism is closely related to both its internal and external environments. Metabolites can act as signal molecules that regulate the functions of genes and proteins, reflecting the status of these environments. This review discusses the metabolism and regulatory functions of O-acetylserine (OAS), S-adenosylmethionine (AdoMet), homocysteine (Hcy), and serine (Ser), which are key metabolites related to sulfur (S)-containing amino acids in plant metabolic networks, in comparison to microbial and animal metabolism. Plants are photosynthetic auxotrophs that have evolved a specific metabolic network different from those in other living organisms. Although amino acids are the building blocks of proteins and common metabolites in all living organisms, their metabolism and regulation in plants have specific features that differ from those in animals and bacteria. In plants, cysteine (Cys), an S-containing amino acid, is synthesized from sulfide and OAS derived from Ser. Methionine (Met), another S-containing amino acid, is also closely related to Ser metabolism because of its thiomethyl moiety. Its S atom is derived from Cys and its methyl group from folates, which are involved in one-carbon metabolism with Ser. One-carbon metabolism is also involved in the biosynthesis of AdoMet, which serves as a methyl donor in the methylation reactions of various biomolecules. Ser is synthesized in three pathways: the phosphorylated pathway found in all organisms and the glycolate and the glycerate pathways, which are specific to plants. Ser metabolism is not only important in Ser supply but also involved in many other functions. Among the metabolites in this network, OAS is known to function as a signal molecule to regulate the expression of OAS gene clusters in response to environmental factors. AdoMet regulates amino acid metabolism at enzymatic and translational levels and regulates gene expression as methyl donor in the DNA and histone methylation or after conversion into bioactive molecules such as polyamine and ethylene. Hcy is involved in Met-AdoMet metabolism and can regulate Ser biosynthesis at an enzymatic level. Ser metabolism is involved in development and stress responses. This review aims to summarize the metabolism and regulatory functions of OAS, AdoMet, Hcy, and Ser and compare the available knowledge for plants with that for animals and bacteria and propose a future perspective on plant research.

Protein interaction patterns in Arabidopsis thaliana leaf mitochondria change in dependence to light

Mitochondrial biology is underpinned by the presence and activity of large protein assemblies participating in the organelle-located steps of respiration, TCA-cycle, glycine oxidation, and oxidative phosphorylation. While the enzymatic roles of these complexes are undisputed, little is known about the interactions of the subunits beyond their presence in these protein complexes and their functions in regulating mitochondrial metabolism. By applying one of the most important regulatory cues for plant metabolism, the presence or absence of light, we here assess changes in the composition and molecular mass of protein assemblies involved in NADH-production in the mitochondrial matrix and in oxidative phosphorylation by employing a differential complexome profiling strategy. Covering a mass up to 25 MDa, we demonstrate dynamic associations of matrix enzymes and of components involved in oxidative phosphorylation. The data presented here form the basis for future studies aiming to advance our understanding of the role of protein:protein interactions in regulating plant mitochondrial functions.

Transcriptome Analysis Reveals Genes of Flooding-Tolerant and Flooding-Sensitive Rapeseeds Differentially Respond to Flooding at the Germination Stage

Flooding results in significant crop yield losses due to exposure of plants to hypoxic stress. Various studies have reported the effect of flooding stress at seedling establishment or later stages. However, the molecular mechanism prevailing at the germination stage under flooding stress remains enigmatic. The present study highlights the comparative transcriptome analysis in two rapeseed lines, i.e., flooding-tolerant (Santana) and -sensitive (23651) lines under control and 6-h flooding treatments at the germination stage. A total of 1840 up-regulated and 1301 down-regulated genes were shared by both lines in response to flooding. There were 4410 differentially expressed genes (DEGs) with increased expression and 4271 DEGs with reduced expression shared in both control and flooding conditions. Gene ontology (GO) enrichment analysis revealed that “transcription regulation”, “structural constituent of cell wall”, “reactive oxygen species metabolic”, “peroxidase”, oxidoreductase”, and “antioxidant activity” were the common processes in rapeseed flooding response. In addition, the processes such as “hormone-mediated signaling pathway”, “response to organic substance response”, “motor activity”, and “microtubule-based process” are likely to confer rapeseed flooding resistance. Mclust analysis clustered DEGs into nine modules; genes in each module shared similar expression patterns and many of these genes overlapped with the top 20 DEGs in some groups. This work provides a comprehensive insight into gene responses and the regulatory network in rapeseed flooding stress and provides guidelines for probing the underlying molecular mechanisms in flooding resistance.

Co-overexpression of AtSHMT1 and AtFDH induces sugar synthesis and enhances the role of original pathways during formaldehyde metabolism in tobacco

Serine hydroxymethyltransferase 1 (SHMT1) is a key enzyme in the photorespiration pathway in higher plants. Our previous study showed that AtSHMT1 controls the assimilation of HCHO to sugars in Arabidopsis. The expression of SHMT1 was induced in Arabidopsis but was inhibited in tobacco under HCHO stress. To investigate whether the function of AtSHMT1 in the HCHO assimilation could be exerted in tobacco, AtSHMT1 was overexpressed alone (S5) or co-overexpressed (SF6) with Arabidopsis formate dehydrogenase (AtFDH) in leaves using a light-inducible promoter in this study. 13C NMR analyses showed that the 13C-metabolic flux from H13CHO was introduced to sugar synthesis in SF6 leaves but not in S5 leaves. The increase in the production of metabolites via the original pathways was particularly greater in SF6 leaves than in S5 leaves, suggesting that co-overexpression of AtSHMT1 and AtFDH is more effective than overexpression of AtSHMT1 alone in the enhancement of HCHO metabolism in tobacco leaves. Consequently, the increase in HCHO uptake and resistance was greater in SF6 leaves than in S5 leaves. The mechanism underlying the role of overexpressed AtSHMT1 and AtFDH was discussed based on changes in photosynthetic parameters, chlorophyll content, antioxidant enzyme activity and the oxidative level in leaves.

Comparative Time-Course Physiological Responses and Proteomic Analysis of Melatonin Priming on Promoting Germination in Aged Oat (Avena sativa L.) Seeds

Melatonin priming is an effective strategy to improve the germination of aged oat (Avena sativa L.) seeds, but the mechanism involved in its time-course responses has remained largely unknown. In the present study, the phenotypic differences, ultrastructural changes, physiological characteristics, and proteomic profiles were examined in aged and melatonin-primed seed (with 10 μM melatonin treatment for 12, 24, and 36 h). Thus, 36 h priming (T36) had a better remediation effect on aged seeds, reflecting in the improved germinability and seedlings, relatively intact cell ultrastructures, and enhanced antioxidant capacity. Proteomic analysis revealed 201 differentially abundant proteins between aged and T36 seeds, of which 96 were up-accumulated. In melatonin-primed seeds, the restoration of membrane integrity by improved antioxidant capacity, which was affected by the stimulation of jasmonic acid synthesis via up-accumulation of 12-oxo-phytodienoic acid reductase, might be a candidate mechanism. Moreover, the relatively intact ultrastructures enabled amino acid metabolism and phenylpropanoid biosynthesis, which were closely associated with energy generation through intermediates of pyruvate, phosphoenolpyruvate, fumarate, and α-ketoglutarate, thus providing energy, active amino acids, and secondary metabolites necessary for germination improvement of aged seeds. These findings clarify the time-course related pathways associated with melatonin priming on promoting the germination of aged oat seeds.

Stoichiometry of two plant glycine decarboxylase complexes and comparison with a cyanobacterial glycine cleavage system

The multienzyme glycine cleavage system (GCS) converts glycine and tetrahydrofolate to the one-carbon compound 5,10-methylenetetrahydrofolate, which is of vital importance for most if not all organisms. Photorespiring plant mitochondria contain very high levels of GCS proteins organised as a fragile glycine decarboxylase complex (GDC). The aim of this study is to provide mass spectrometry-based stoichiometric data for the plant leaf GDC and examine whether complex formation could be a general property of the GCS in photosynthesizing organisms. The molar ratios of the leaf GDC component proteins are 1L2 -4P2 -8T-26H and 1L2 -4P2 -8T-20H for pea and Arabidopsis, respectively, as determined by mass spectrometry. The minimum mass of the plant leaf GDC ranges from 1550 to 1650 kDa, which is larger than previously assumed. The Arabidopsis GDC contains four times more of the isoforms GCS-P1 and GCS-L1 in comparison with GCS-P2 and GCS-L2, respectively, whereas the H-isoproteins GCS-H1 and GCS-H3 are fully redundant as indicated by their about equal amounts. Isoform GCS-H2 is not present in leaf mitochondria. In the cyanobacterium Synechocystis sp. PCC 6803, GCS proteins concentrations are low but above the complex formation threshold reported for pea leaf GDC. Indeed, formation of a cyanobacterial GDC from the individual recombinant GCS proteins in vitro could be demonstrated. Presence and metabolic significance of a Synechocystis GDC in vivo remain to be examined but could involve multimers of the GCS H-protein that dynamically crosslink the three GCS enzyme proteins, facilitating glycine metabolism by the formation of multienzyme metabolic complexes. Data are available via ProteomeXchange with identifier PXD018211.

Mutation in OsCADT1 enhances cadmium tolerance and enriches selenium in rice grain

How cadmium (Cd) tolerance in rice is regulated remains poorly understood. We used a forward genetic approach to investigate Cd tolerance in rice. Using a root elongation assay, we isolated a rice mutant with enhanced Cd tolerance, cadt1, from an ethyl methanesulphonate (EMS)-mutagenized population of a widely grown Indica cultivar. The mutant accumulated more Cd in roots but not in shoots and grains. Using genomic resequencing and complementation, we identified OsCADT1 as the causal gene for the mutant phenotype, which encodes a putative serine hydroxymethyltransferase. OsCADT1 protein was localized to the nucleus and the OsCADT1 gene was expressed in both roots and shoots. OsCADT1 mutation resulted in higher sulphur and selenium accumulation in the shoots and grains. Selenate influx in cadt1 was 2.4 times that of the wild-type. The mutant showed higher expression of the sulphate/selenate transporter gene OsSULTR1;1 and the sulphur-deficiency-inducible gene OsSDI1. Thiol compounds including cysteine, glutathione and phytochelatins were significantly increased in the mutant, underlying its increased Cd tolerance. Growth and grain biomass were little affected. The results suggest that OsCADT1 acts as a negative regulator of sulphate/selenate uptake and assimilation. OsCADT1 mutation increases Cd tolerance and enriches selenium in rice grains, providing a novel solution for selenium biofortification.

Melatonin Priming Alleviates Aging-Induced Germination Inhibition by Regulating β-oxidation, Protein Translation, and Antioxidant Metabolism in Oat (Avena sativa L.) Seeds

Although melatonin has been reported to play an important role in regulating metabolic events under adverse stresses, its underlying mechanisms on germination in aged seeds remain unclear. This study was conducted to investigate the effect of melatonin priming (MP) on embryos of aged oat seeds in relation to germination, ultrastructural changes, antioxidant responses, and protein profiles. Proteomic analysis revealed, in total, 402 differentially expressed proteins (DEPs) in normal, aged, and aged + MP embryos. The downregulated DEPs in aged embryos were enriched in sucrose metabolism, glycolysis, β-oxidation of lipid, and protein synthesis. MP (200 μM) turned four downregulated DEPs into upregulated DEPs, among which, especially 3-ketoacyl-CoA thiolase-like protein (KATLP) involved in the β-oxidation pathway played a key role in maintaining TCA cycle stability and providing more energy for protein translation. Furthermore, it was found that MP enhanced antioxidant capacity in the ascorbate-glutathione (AsA-GSH) system, declined reactive oxygen species (ROS), and improved cell ultrastructure. These results indicated that the impaired germination and seedling growth of aged seeds could be rescued to a certain level by melatonin, predominantly depending on β-oxidation, protein translation, and antioxidant protection of AsA-GSH. This work reveals new insights into melatonin-mediated mechanisms from protein profiles that occur in embryos of oat seeds processed by both aging and priming.

Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

Mitochondria host vital cellular functions, including oxidative phosphorylation and co-factor biosynthesis, which are reflected in their proteome. At the cellular level plant mitochondria are organized into hundreds of discrete functional entities, which undergo dynamic fission and fusion. It is the individual organelle that operates in the living cell, yet biochemical and physiological assessments have exclusively focused on the characteristics of large populations of mitochondria. Here, we explore the protein composition of an individual average plant mitochondrion to deduce principles of functional and structural organisation. We perform proteomics on purified mitochondria from cultured heterotrophic Arabidopsis cells with intensity-based absolute quantification and scale the dataset to the single organelle based on criteria that are justified by experimental evidence and theoretical considerations. We estimate that a total of 1.4 million protein molecules make up a single Arabidopsis mitochondrion on average. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40 000 for Voltage-Dependent Anion Channel 1 to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat proteins that modify mitochondrial transcripts. For our analysis, we consider the physical and chemical constraints of the single organelle and discuss prominent features of mitochondrial architecture, protein biogenesis, oxidative phosphorylation, metabolism, antioxidant defence, genome maintenance, gene expression, and dynamics. While assessing the limitations of our considerations, we exemplify how our understanding of biochemical function and structural organization of plant mitochondria can be connected in order to obtain global and specific insights into how organelles work.

Lysine, Lysine-Rich, Serine, and Serine-Rich Proteins: Link Between Metabolism, Development, and Abiotic Stress Tolerance and the Role of ncRNAs in Their Regulation

Lysine (Lys) is indispensable nutritionally, and its levels in plants are modulated by both transcriptional and post-transcriptional control during plant ontogeny. Animal glutamate receptor homologs have been detected in plants, which may participate in several plant processes through the Lys catabolic products. Interestingly, a connection between Lys and serotonin metabolism has been established recently in rice. 2-Aminoadipate, a catabolic product of Lys appears to play a critical role between serotonin accumulation and the color of rice endosperm/grain. It has also been shown that expression of some lysine-methylated proteins and genes encoding lysine-methyltransferases (KMTs) are regulated by cadmium even as it is known that Lys biosynthesis and its degradation are modulated by novel mechanisms. Three complex pathways co-exist in plants for serine (Ser) biosynthesis, and the relative preponderance of each pathway in relation to plant development or abiotic stress tolerance are being unfolded slowly. But the phosphorylated pathway of L-Ser biosynthesis (PPSB) appears to play critical roles and is essential in plant metabolism and development. Ser, which participates indirectly in purine and pyrimidine biosynthesis and plays a pivotal role in plant metabolism and signaling. Also, L-Ser has been implicated in plant responses to both biotic and abiotic stresses. A large body of information implicates Lys-rich and serine/arginine-rich (SR) proteins in a very wide array of abiotic stresses. Interestingly, a link exists between Lys-rich K-segment and stress tolerance levels. It is of interest to note that abiotic stresses largely influence the expression patterns of SR proteins and also the alternative splicing (AS) patterns. We have checked if any lncRNAs form a cohort of differentially expressed genes from the publicly available PPSB, sequence read archives of NCBI GenBank. Finally, we discuss the link between Lys and Ser synthesis, catabolism, Lys-proteins, and SR proteins during plant development and their myriad roles in response to abiotic stresses.

Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5

Chickpea production may be seriously threatened by Fusarium wilt, a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. ciceris. F. oxysporum race 5 is the most important race in the Mediterranean basin. Recently, the region responsible for resistance race 5 has been delimited within a region on chromosome 2 that spans 820 kb. To gain a better understanding of this genomic region, we used a transcriptomic approach based on quantitative real-time PCR to analyze the expression profiles of 22 selected candidate genes. We used a pair of near-isogenic lines (NILs) differing in their sensitivity to Fusarium race 5 (resistant vs susceptible) to monitor the transcriptional changes over a time-course experiment (24, 48, and 72 hours post inoculation, hpi). Qualitative differences occurred during the timing of regulation. A cluster of 12 genes were induced by the resistant NIL at 24 hpi, whereas a second cluster contained 9 genes induced by the susceptible NIL at 48 hpi. Their possible functions in the molecular defence of chickpea is discussed. Our study provides new insight into the molecular defence against Fusarium race 5 and demonstrates that development of NILs is a rich resource to facilitate the detection of candidate genes. The new genes regulated here may be useful against other Fusarium races.

Photorespiratory serine hydroxymethyltransferase 1 activity impacts abiotic stress tolerance and stomatal closure

The photorespiratory cycle is a crucial pathway in photosynthetic organisms because it removes toxic 2-phosphoglycolate made by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase and retrieves its carbon as 3-phosphoglycerate. Mitochondrial serine hydroxymethyltransferase 1 (SHMT1) is an essential photorespiratory enzyme converting glycine to serine. SHMT1 regulation remains poorly understood although it could involve the phosphorylation of serine 31. Here, we report the complementation of Arabidopsis thaliana shm1-1 by SHMT1 wild-type, phosphorylation-mimetic (S31D) or nonphophorylatable (S31A) forms. All SHMT1 forms could almost fully complement the photorespiratory growth phenotype of shm1-1; however, each transgenic line had only 50% of normal SHMT activity. In response to either a salt or drought stress, Compl-S31D lines showed a more severe growth deficiency compared with the other transgenic lines. This sensitivity to salt appeared to reflect reduced SHMT1-S31D protein amounts and a lower activity that impacted leaf metabolism leading to proline underaccumulation and overaccumulation of polyamines. The S31D mutation in SHMT1 also led to a reduction in salt-induced and ABA-induced stomatal closure. Taken together, our results highlight the importance of maintaining photorespiratory SHMT1 activity in salt and drought stress conditions and indicate that SHMT1 S31 phosphorylation could be involved in modulating SHMT1 protein stability.

Mechanistic understanding of photorespiration paves the way to a new green revolution

Photorespiration is frequently considered a wasteful and inefficient process. However, mutant analysis demonstrated that photorespiration is essential for recycling of 2-phosphoglycolate in C₃ and C₄ land plants, in algae, and even in cyanobacteria operating carboxysome-based carbon (C) concentrating mechanisms. Photorespiration links photosynthetic C assimilation with other metabolic processes, such as nitrogen and sulfur assimilation, as well as C₁ metabolism, and it may contribute to balancing the redox poise between chloroplasts, peroxisomes, mitochondria and cytoplasm. The high degree of metabolic interdependencies and the pleiotropic phenotypes of photorespiratory mutants impedes the distinction between core and accessory functions. Newly developed synthetic bypasses of photorespiration, beyond holding potential for significant yield increases in C₃ crops, will enable us to differentiate between essential and accessory functions of photorespiration.

Knock-Down of the Phosphoserine Phosphatase Gene Effects Rather N- Than S-Metabolism in Arabidopsis thaliana

The aim of present study was to elucidate the significance of the phosphorylated pathway of Ser production for Cys biosynthesis in leaves at day and night and upon cadmium (Cd) exposure. For this purpose, Arabidopsis wildtype plants as control and its psp mutant knocked-down in phosphoserine phosphatase (PSP) were used to test if (i) photorespiratory Ser is the dominant precursor of Cys synthesis in autotrophic tissue in the light, (ii) the phosphorylated pathway of Ser production can take over Ser biosynthesis in leaves at night, and (iii) Cd exposure stimulates Cys and glutathione (GSH) biosynthesis and effects the crosstalk of S and N metabolism, irrespective of the Ser source. Glycine (Gly) and Ser contents were not affected by reduction of the psp transcript level confirming that the photorespiratory pathway is the main route of Ser synthesis. The reduction of the PSP transcript level in the mutant did not affect day/night regulation of sulfur fluxes while day/night fluctuation of sulfur metabolite amounts were no longer observed, presumably due to slower turnover of sulfur metabolites in the mutant. Enhanced contents of non-protein thiols in both genotypes and of GSH only in the psp mutant were observed upon Cd treatment. Mutation of the phosphorylated pathway of Ser biosynthesis caused an accumulation of alanine, aspartate, lysine and a decrease of branched-chain amino acids. Knock-down of the PSP gene induced additional defense mechanisms against Cd toxicity that differ from those of WT plants.

The Photorespiratory BOU Gene Mutation Alters Sulfur Assimilation and Its Crosstalk With Carbon and Nitrogen Metabolism in Arabidopsis thaliana

This study was aimed at elucidating the significance of photorespiratory serine (Ser) production for cysteine (Cys) biosynthesis. For this purpose, sulfur (S) metabolism and its crosstalk with nitrogen (N) and carbon (C) metabolism were analyzed in wildtype Arabidopsis and its photorespiratory bou-2 mutant with impaired glycine decarboxylase (GDC) activity. Foliar glycine and Ser contents were enhanced in the mutant at day and night. The high Ser levels in the mutant cannot be explained by transcript abundances of genes of the photorespiratory pathway or two alternative pathways of Ser biosynthesis. Despite enhanced foliar Ser, reduced GDC activity mediated a decline in sulfur flux into major sulfur pools in the mutant, as a result of deregulation of genes of sulfur reduction and assimilation. Still, foliar Cys and glutathione contents in the mutant were enhanced. The use of Cys for methionine and glucosinolates synthesis was reduced in the mutant. Reduced GDC activity in the mutant downregulated Calvin Cycle and nitrogen assimilation genes, upregulated key enzymes of glycolysis and the tricarboxylic acid (TCA) pathway and modified accumulation of sugars and TCA intermediates. Thus, photorespiratory Ser production can be replaced by other metabolic Ser sources, but this replacement deregulates the cross-talk between S, N, and C metabolism.

The Combined Loss of Triose Phosphate and Xylulose 5-Phosphate/Phosphate Translocators Leads to Severe Growth Retardation and Impaired Photosynthesis in Arabidopsis thaliana tpt/xpt Double Mutants

The xylulose 5-phosphate/phosphate translocator (XPT) represents the fourth functional member of the phosphate translocator (PT) family residing in the plastid inner envelope membrane. In contrast to the other three members, little is known on the physiological role of the XPT. Based on its major transport substrates (i.e., pentose phosphates) the XPT has been proposed to act as a link between the plastidial and extraplastidial branches of the oxidative pentose phosphate pathway (OPPP). As the XPT is also capable of transporting triose phosphates, it might as well support the triose phosphate PT (TPT) in exporting photoassimilates from the chloroplast in the light ('day path of carbon') and hence in supplying the whole plant with carbohydrates. Two independent knockout mutant alleles of the XPT (xpt-1 and xpt-2) lacked any specific phenotype, suggesting that the XPT function is redundant. However, double mutants generated from crossings of xpt-1 to different mutant alleles of the TPT (tpt-1 and tpt-2) were severely retarded in size, exhibited a high chlorophyll fluorescence phenotype, and impaired photosynthetic electron transport rates. In the double mutant the export of triose phosphates from the chloroplasts is completely blocked. Hence, precursors for sucrose biosynthesis derive entirely from starch turnover ('night path of carbon'), which was accompanied by a marked accumulation of maltose as a starch breakdown product. Moreover, pentose phosphates produced by the extraplastidial branch of the OPPP also accumulated in the double mutants. Thus, an active XPT indeed retrieves excessive pentose phosphates from the extra-plastidial space and makes them available to the plastids. Further metabolic profiling revealed that phosphorylated intermediates remained largely unaffected, whereas fumarate and glycine contents were diminished in the double mutants. The assessment of C/N-ratios suggested co-limitations of C- and N-metabolism as possible cause for growth retardation of the double mutants. Feeding of sucrose partially rescued the growth and photosynthesis phenotypes of the double mutants. Immunoblots of thylakoid proteins, spectroscopic determinations of photosynthesis complexes, and chlorophyll a fluorescence emission spectra at 77 Kelvin could only partially explain constrains in photosynthesis observed in the double mutants. The data are discussed together with aspects of the OPPP and central carbon metabolism.

The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism

Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate - serine pathway) is initiated in the cytosol and involves glycerate formation from 3-phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume

Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity (I^∗ = 0.575, h^∗ = 0.393) was higher than the genetic diversity (I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width.

T-protein is present in large excess over the other proteins of the glycine cleavage system in leaves of Arabidopsis

T-protein is present in large excess over the other proteins of the glycine cleavage system in leaves of Arabidopsis and therefore, exerts little control over the photorespiratory pathway. T-protein is the aminomethyltransferase of the glycine cleavage multienzyme system (GCS), also known as the glycine decarboxylase complex, and essential for photorespiration and one-carbon metabolism. Here, we studied what effects varying levels of the GCS T-protein would have on GCS activity, the operation of the photorespiratory pathway, photosynthesis, and plant growth. To this end, we examined Arabidopsis thaliana T-protein overexpression lines with up to threefold higher amounts of leaf T-protein as well as one knockdown mutant with about 5% residual leaf T-protein and one knockout mutant. Overexpression did not alter photosynthetic CO₂ uptake and plant growth, and the knockout mutation was lethal even in the non-photorespiratory environment of air enriched to 1% CO₂. Unexpectedly in light of this very low T-protein content, however, the knockdown mutant was able to grow and propagate in normal air and displayed only some minor changes, such as a moderate glycine accumulation in combination with somewhat delayed growth. Neither overexpression nor the knockdown of T-protein altered the amounts of the other three GCS proteins, suggesting that the biosynthesis of the GCS proteins is not synchronized at this level. We also observed that the knockdown causes less T-protein mostly in leaf mesophyll cells, but not so much in the vasculature, and discuss this phenomenon in light of the dual involvement of the GCS and hence T-protein in plant metabolism. Collectively, this work shows that T-protein is present in large excess over the other proteins of the glycine cleavage system in leaves of Arabidopsis and therefore exerts little control over the photorespiratory pathway.

The Effect of Single and Multiple SERAT Mutants on Serine and Sulfur Metabolism

The gene family of serine acetyltransferases (SERATs) constitutes an interface between the plant pathways of serine and sulfur metabolism. SERATs provide the activated precursor, O-acetylserine for the fixation of reduced sulfur into cysteine by exchanging the serine hydroxyl moiety by a sulfhydryl moiety, and subsequently all organic compounds containing reduced sulfur moieties. We investigate here, how manipulation of the SERAT interface results in metabolic alterations upstream or downstream of this boundary and the extent to which the five SERAT isoforms exert an effect on the coupled system, respectively. Serine is synthesized through three distinct pathways while cysteine biosynthesis is distributed over the three compartments cytosol, mitochondria, and plastids. As the respective mutants are viable, all necessary metabolites can obviously cross various membrane systems to compensate what would otherwise constitute a lethal failure in cysteine biosynthesis. Furthermore, given that cysteine serves as precursor for multiple pathways, cysteine biosynthesis is highly regulated at both, the enzyme and the expression level. In this study, metabolite profiles of a mutant series of the SERAT gene family displayed that levels of the downstream metabolites in sulfur metabolism were affected in correlation with the reduction levels of SERAT activities and the growth phenotypes, while levels of the upstream metabolites in serine metabolism were unchanged in the serat mutants compared to wild-type plants. These results suggest that despite of the fact that the two metabolic pathways are directly connected, there seems to be no causal link in metabolic alterations. This might be caused by the difference of their pool sizes or the tight regulation by homeostatic mechanisms that control the metabolite concentration in plant cells. Additionally, growth conditions exerted an influence on metabolic compositions.

Investigating the Role of the Photorespiratory Pathway in Non-photosynthetic Tissues

Whilst photorespiration represents one of the dominant pathway fluxes in photosynthetic tissues there are hints from publically available gene expression data such as that housed in the bioarray resource (BAR; www.bar.utoronto.ca) that several of the constituent enzymes are present in roots and other heterotrophic tissues. Here we describe a protocol based on modification of the gaseous environment surrounding individual tissues of mutant and wild type Arabidopsis and evaluation of the consequences. This method could additionally easily be used for larger plants.

Measurement of Enzyme Activities

The determination of enzyme activities in organ or organellar extracts is an important means of investigating metabolic networks and allows testing the success of enzyme-targeted genetic engineering. It also delivers information on intrinsic enzyme parameters such as kinetic properties or impact of effector molecules. This chapter provides protocols on how to assess activities of the enzymes of the core photorespiratory pathway, from 2-phosphoglycolate phosphatase to glycerate 3-kinase.

Measurement of Transcripts Associated with Photorespiration and Related Redox Signaling

To study photorespiration and to characterize related components, gene expression analysis is a central approach. An overview of the experimental setup, protocols, and methods we use to investigate photorespiration-associated gene expression is presented. Within this chapter, we describe simple procedures to experimentally alter the photorespiratory flux and provide protocols for transcriptomic analysis with a focus on genes encoding photorespiratory proteins as well as those induced by photorespiratory hydrogen peroxide (H₂O₂). Examples of typical results are presented and their significance to understanding redox signaling is discussed.

Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana

Sulphur (S) is an essential element for all living organisms. The uptake, assimilation and metabolism of S in plants are well studied. However, the regulation of S homeostasis remains largely unknown. Here, we report on the identification and characterisation of the more sulphur accumulation1 (msa1-1) mutant. The MSA1 protein is localized to the nucleus and is required for both S-adenosylmethionine (SAM) production and DNA methylation. Loss of function of the nuclear localised MSA1 leads to a reduction in SAM in roots and a strong S-deficiency response even at ample S supply, causing an over-accumulation of sulphate, sulphite, cysteine and glutathione. Supplementation with SAM suppresses this high S phenotype. Furthermore, mutation of MSA1 affects genome-wide DNA methylation, including the methylation of S-deficiency responsive genes. Elevated S accumulation in msa1-1 requires the increased expression of the sulphate transporter genes SULTR1;1 and SULTR1;2 which are also differentially methylated in msa1-1. Our results suggest a novel function for MSA1 in the nucleus in regulating SAM biosynthesis and maintaining S homeostasis epigenetically via DNA methylation.

Sulphur is an essential element for all living organisms including plants. Plants take up sulphur from the soil mainly in the form of inorganic sulphate. The uptake of sulphate and assimilation of sulphur have been well studied. However, the regulation of sulphur accumulation in plants remains largely unknown. In this study, we characterize the high leaf sulphur mutant more sulphur accumulation1 (msa1-1) and demonstrate the function of MSA1 in controlling sulphur accumulation in Arabidopsis thaliana. The MSA1 protein is localized to the nucleus and is required for the biosynthesis of S-adenosylmethionine (SAM) which is a universal methyl donor for many methylation reactions, including DNA methylation. Loss of function of MSA1 reduces the SAM level in roots and affects genome-wide DNA methylation, including the methylation of sulphate transporter genes. We show that the high sulphur phenotype of msa1-1 requires elevated expression of the sulphate transporter genes which are differentially methylated in msa1-1. Our results suggest a connection between sulphur homeostasis and DNA methylation that is mediated by MSA1.

Decreased glycolate oxidase activity leads to altered carbon allocation and leaf senescence after a transfer from high CO2 to ambient air in Arabidopsis thaliana

Metabolic and physiological analyses of Arabidopsis thaliana glycolate oxidase (GOX) mutant leaves were performed to understand the development of the photorespiratory phenotype after transfer from high CO2 to air. We show that two Arabidopsis genes, GOX1 and GOX2, share a redundant photorespiratory role. Air-grown single gox1 and gox2 mutants grew normally and no significant differences in leaf metabolic levels and photosynthetic activities were found when compared with wild-type plants. To study the impact of a highly reduced GOX activity on plant metabolism, both GOX1 and GOX2 expression was knocked-down using an artificial miRNA strategy. Air-grown amiRgox1/2 plants with a residual 5% GOX activity exhibited a severe growth phenotype. When high-CO2-grown adult plants were transferred to air, the photosynthetic activity of amiRgox1/2 was rapidly reduced to 50% of control levels, and a high non-photochemical chlorophyll fluorescence quenching was maintained. (13)C-labeling revealed that daily assimilated carbon accumulated in glycolate, leading to reduced carbon allocation to sugars, organic acids, and amino acids. Such changes were not always mirrored in leaf total metabolite levels, since many soluble amino acids increased after transfer, while total soluble protein, RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase), and chlorophyll amounts decreased in amiRgox1/2 plants. The senescence marker, SAG12, was induced only in amiRgox1/2 rosettes after transfer to air. The expression of maize photorespiratory GOX in amiRgox1/2 abolished all observed phenotypes. The results indicate that the inhibition of the photorespiratory cycle negatively impacts photosynthesis, alters carbon allocation, and leads to early senescence in old rosette leaves.

On the metabolic interactions of (photo)respiration

Given that photorespiration is inextricably linked to the process of photosynthesis by virtue of sharing the common first enzyme Rubisco, the photorespiratory pathway has been less subject to study in isolation than many other metabolic pathways. That said, despite often being described to be linked to reactions of ammonia assimilation, C1 metabolism and respiratory metabolism, the precise molecular mechanisms governing these linkages in land plants remain partially obscure. The application of broad metabolite profiling on mutants with altered levels of metabolic enzymes has facilitated the identification of common and distinct metabolic responses among them. Here we provide an update of the recent findings from such studies, focusing particularly on the interplay between photorespiration and the metabolic reactions of mitochondrial respiration. In order to do so we evaluated (i) changes in organic acids following environmental perturbation of metabolism, (ii) changes in organic acid levels in a wide range of photorespiratory mutants, (iii) changes in levels of photorespiratory metabolites in transgenic tomato lines deficient in the expression of enzymes of the tricarboxylic acid cycle. In addition, we estimated the rates of photorespiration in a complete set of tricarboxylic acid cycle transgenic tomato lines. Finally, we discuss insight concerning the interaction between photorespiration and other pathways that has been attained following the development of (13)CO2-based flux profiling methods.

Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network

Photorespiration is an essential high flux metabolic pathway that is found in all oxygen-producing photosynthetic organisms. It is often viewed as a closed metabolic repair pathway that serves to detoxify 2-phosphoglycolic acid and to recycle carbon to fuel the Calvin-Benson cycle. However, this view is too simplistic since the photorespiratory cycle is known to interact with several primary metabolic pathways, including photosynthesis, nitrate assimilation, amino acid metabolism, C1 metabolism and the Krebs (TCA) cycle. Here we will review recent advances in photorespiration research and discuss future priorities to better understand (i) the metabolic integration of the photorespiratory cycle within the complex network of plant primary metabolism and (ii) the importance of photorespiration in response to abiotic and biotic stresses.

Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria

The plant growth-promoting rhizobacterium (PGPR) Pseudomonas simiae WCS417r stimulates lateral root formation and increases shoot growth in Arabidopsis thaliana (Arabidopsis). These plant growth-stimulating effects are partly caused by volatile organic compounds (VOCs) produced by the bacterium. Here, we performed a genome-wide association (GWA) study on natural genetic variation in Arabidopsis for the ability to profit from rhizobacteria-mediated plant growth-promotion. To this end, 302 Arabidopsis accessions were tested for root architecture characteristics and shoot fresh weight in response to exposure to WCS417r. Although virtually all Arabidopsis accessions tested responded positively to WCS417r, there was a large variation between accessions in the increase in shoot fresh weight, the extra number of lateral roots formed, and the effect on primary root length. Correlation analyses revealed that the bacterially-mediated increase in shoot fresh weight is related to alterations in root architecture. GWA mapping for WCS417r-stimulated changes in root and shoot growth characteristics revealed 10 genetic loci highly associated with the responsiveness of Arabidopsis to the plant growth-promoting activity of WCS417r. Several of the underlying candidate genes have been implicated in important plant growth-related processes. These results demonstrate that plants possess natural genetic variation for the capacity to profit from the plant growth-promoting function of a beneficial rhizobacterium in their rhizosphere. This knowledge is a promising starting point for sustainable breeding strategies for future crops that are better able to maximize profitable functions from their root microbiome.

Soybean Cyst Nematode Resistance Emerged via Artificial Selection of Duplicated Serine Hydroxymethyltransferase Genes

A major soybean (Forrest cultivar) quantitative trait locus (QTL) gene, Rhg4, which controls resistance to soybean cyst nematodes (SCN), encodes the enzyme serine hydroxylmethyltransferase (SHMT). The resistant allele possesses two critical missense mutations (P130R and N358Y) compared to that of the sensitive allele, rhg4. To understand the evolutionary history of this gene, sequences of 117 SHMT family members from 18 representative plant species were used to reconstruct their phylogeny. According to this phylogeny, the plant SHMT gene family can be divided into two groups and four subgroups (Ia, Ib, IIa, and IIb). Belonging to the Subgroup Ia lineage, the rhg4 gene evolved from a recent duplication event in Glycine sp.. To further explore how the SCN-resistant allele emerged, both the rhg4 gene and its closest homolog, the rhg4h gene, were isolated from 33 cultivated and 68 wild soybean varieties. The results suggested that after gene duplication, the soybean rhg4 gene accumulated a higher number of non-synonymous mutations than rhg4h. Although a higher number of segregating sites and gene haplotypes were detected in wild soybeans than in cultivars, the SCN-resistant Rhg4 allele (represented by haplotype 4) was not found in wild varieties. Instead, a very similar allele, haplotype 3, was observed in wild soybeans at a frequency of 7.4%, although it lacked the two critical non-synonymous substitutions. Taken together, these findings support that the SCN-resistant Rhg4 allele likely emerged via artificial selection during the soybean domestication process, based on a SCN-sensitive allele inherited from wild soybeans.

A metabolomics study delineating geographical location-associated primary metabolic changes in the leaves of growing tobacco plants by GC-MS and CE-MS

Ecological conditions and developmental senescence significantly affect the physiological metabolism of plants, yet relatively little is known about the influence of geographical location on dynamic changes in plant leaves during growth. Pseudotargeted gas chromatography-selected ion monitoring-mass spectrometry and capillary electrophoresis-mass spectrometry were used to investigate a time course of the metabolic responses of tobacco leaves to geographical location. Principal component analysis revealed obvious metabolic discrimination between growing districts relative to cultivars. A complex carbon and nitrogen metabolic network was modulated by environmental factors during growth. When the Xuchang and Dali Districts in China were compared, the results indicated that higher rates of photosynthesis, photorespiration and respiration were utilized in Xuchang District to generate the energy and carbon skeletons needed for the biosynthesis of nitrogen-containing metabolites. The increased abundance of defense-associated metabolites generated from the shikimate-phenylpropanoid pathway in Xuchang relative to Dali was implicated in protection against stress.

Characterization and molecular cloning of a serine hydroxymethyltransferase 1 (OsSHM1) in rice

Serine hydroxymethyltransferase (SHMT) is important for one carbon metabolism and photorespiration in higher plants for its participation in plant growth and development, and resistance to biotic and abiotic stresses. A rice serine hydroxymethyltransferase gene, OsSHM1, an ortholog of Arabidopsis SHM1, was isolated using map-based cloning. The osshm1 mutant had chlorotic lesions and a considerably smaller, lethal phenotype under natural ambient CO2 concentrations, but could be restored to wild type with normal growth under elevated CO2 levels (0.5% CO2 ), showing a typical photorespiratory phenotype. The data from antioxidant enzymes activity measurement suggested that osshm1 was subjected to significant oxidative stress. Also, OsSHM1 was expressed in all organs tested (root, culm, leaf, and young panicle) but predominantly in leaves. OsSHM1 protein is localized to the mitochondria. Our study suggested that molecular function of the OsSHM1 gene is conserved in rice and Arabidopsis.

D-2-hydroxyglutarate metabolism is linked to photorespiration in the shm1-1 mutant

The Arabidopsis mutant shm1-1 is defective in mitochondrial serine hydroxymethyltransferase 1 activity and displays a lethal photorespiratory phenotype at ambient CO2 concentration but grows normally at high CO2 . After transferring high CO2 -grown shm1-1 plants to ambient CO2 , the younger leaves remain photosynthetically active while developed leaves display increased yellowing and decreased FV /FM values. Metabolite analysis of plants transferred from high CO2 to ambient air indicates a massive light-dependent (photorespiratory) accumulation of glycine, 2-oxoglutarate (2OG) and D-2-hydroxyglutarate (D-2HG). Amino acid markers of senescence accumulated in ambient air in wild-type and shm1-1 plants maintained in darkness and also build up in shm1-1 in the light. This, together with an enhanced transcription of the senescence marker SAG12 in shm1-1, suggests the initiation of senescence in shm1-1 under photorespiratory conditions. Mitochondrial D-2HG dehydrogenase (D-2HGDH) converts D-2HG into 2OG. In vitro studies indicate that 2OG exerts competitive inhibition on D-2HGDH with a Ki of 1.96 mm. 2OG is therefore a suitable candidate as inhibitor of the in vivo D-2HGDH activity, as 2OG is produced and accumulates in mitochondria. Inhibition of the D-2HGDH by 2OG is likely a mechanism by which D-2HG accumulates in shm1-1, however it cannot be ruled out that D-2HG may also accumulate due to an active senescence programme that is initiated in these plants after transfer to photorespiratory conditions. Thus, a novel interaction of the photorespiratory pathway with cellular processes involving D-2HG has been identified.

New insights into photorespiration obtained from metabolomics

Photorespiration, one of the cornerstone pathways of primary metabolism, allows plant growth in a high oxygen-containing environment. While the oxygenase reaction of Rubisco directly influences photosynthesis per se, several other processes are also affected by photorespiration, including nitrogen assimilation, respiration, amino acid metabolism, 1-C metabolism and redox metabolism, cumulating to impose a severe impact across multiple signalling pathways. Accordingly, although the plant photorespiratory cycle is complex and highly compartmentalised, little is currently known about the participating transport proteins, and relatively few of them have been properly identified. Despite its centrality, uniqueness, and mystery, the biochemistry of photorespiration has historically been quite poorly understood, in part because at least some of its enzymes and intermediates tend to be labile and of low abundance. Fortunately, the integration of molecular and genetic approaches with biochemical ones, such as metabolite profiling, is now driving rapid advances in knowledge of the key metabolic roles and connections of the enzymes and genes of the photorespiratory pathway. While these experiments have revealed a surprising complexity in the response and established connections between photorespiration and other metabolic pathways, the mechanisms behind the observed responses have still to be fully elucidated. Here we review recent progress into photorespiration and its interaction with other metabolic processes, paying particular attention to data emanating from metabolic profiling studies.

The variety of photorespiratory phenotypes - employing the current status for future research directions on photorespiration

Mutations of genes encoding for proteins within the photorespiratory core cycle and associated processes are characterised by lethality under normal air but viability under elevated CO2 conditions. This feature has been described as 'the photorespiratory phenotype' and assumed to be distinctly equal for all of these mutants. In recent years a broad collection of photorespiratory mutants has been isolated, which has allowed a comparative analysis. Distinct phenotypic features were observed when Arabidopsis thaliana mutants defective in photorespiratory enzymes were compared, and during shifts from elevated to ambient CO2 conditions. The exact reasons for the mutant-specific photorespiratory phenotypes are mostly unknown, but they indicate even more plasticity of photorespiratory metabolism. Moreover, a growing body of evidence was obtained that mutant features could be modulated by alterations of several factors, such as CO2 :O2 ratios, photoperiod, light intensity, organic carbon supply and pathogens. Hence, systematic analyses of the responses to these factors appear to be crucial to unravel mechanisms how photorespiration adapts and interacts with the whole cellular metabolism. Here we review current knowledge regarding photorespiratory mutants and propose a new level of phenotypic sub-classification. Finally, we present further questions that should be addressed in the field of photorespiration.

Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase stability

Protein ubiquitination is a reversible process catalyzed by ubiquitin ligases and ubiquitin-specific proteases (UBPs). We report the identification and characterization of UBP16 in Arabidopsis thaliana. UBP16 is a functional ubiquitin-specific protease and its enzyme activity is required for salt tolerance. Plants lacking UBP16 were hypersensitive to salt stress and accumulated more sodium and less potassium. UBP16 positively regulated plasma membrane Na(+)/H(+) antiport activity. Through yeast two-hybrid screening, we identified a putative target of UBP16, SERINE HYDROXYMETHYLTRANSFERASE1 (SHM1), which has previously been reported to be involved in photorespiration and salt tolerance in Arabidopsis. We found that SHM1 is degraded in a 26S proteasome-dependent process, and UBP16 stabilizes SHM1 by removing the conjugated ubiquitin. Ser hydroxymethyltransferase activity is lower in the ubp16 mutant than in the wild type but higher than in the shm1 mutant. During salt stress, UBP16 and SHM1 function in preventing cell death and reducing reactive oxygen species accumulation, activities that are correlated with increasing Na(+)/H(+) antiport activity. Overexpression of SHM1 in the ubp16 mutant partially rescues its salt-sensitive phenotype. Taken together, our results suggest that UBP16 is involved in salt tolerance in Arabidopsis by modulating sodium transport activity and repressing cell death at least partially through modulating SMH1stability and activity.

High-to-low CO2 acclimation reveals plasticity of the photorespiratory pathway and indicates regulatory links to cellular metabolism of Arabidopsis

BACKGROUND

Photorespiratory carbon metabolism was long considered as an essentially closed and nonregulated pathway with little interaction to other metabolic routes except nitrogen metabolism and respiration. Most mutants of this pathway cannot survive in ambient air and require CO(2)-enriched air for normal growth. Several studies indicate that this CO(2) requirement is very different for individual mutants, suggesting a higher plasticity and more interaction of photorespiratory metabolism as generally thought. To understand this better, we examined a variety of high- and low-level parameters at 1% CO(2) and their alteration during acclimation of wild-type plants and selected photorespiratory mutants to ambient air.

METHODOLOGY AND PRINCIPAL FINDINGS

The wild type and four photorespiratory mutants of Arabidopsis thaliana (Arabidopsis) were grown to a defined stadium at 1% CO(2) and then transferred to normal air (0.038% CO(2)). All other conditions remained unchanged. This approach allowed unbiased side-by-side monitoring of acclimation processes on several levels. For all lines, diel (24 h) leaf growth, photosynthetic gas exchange, and PSII fluorescence were monitored. Metabolite profiling was performed for the wild type and two mutants. During acclimation, considerable variation between the individual genotypes was detected in many of the examined parameters, which correlated with the position of the impaired reaction in the photorespiratory pathway.

CONCLUSIONS

Photorespiratory carbon metabolism does not operate as a fully closed pathway. Acclimation from high to low CO(2) was typically steady and consistent for a number of features over several days, but we also found unexpected short-term events, such as an intermittent very massive rise of glycine levels after transition of one particular mutant to ambient air. We conclude that photorespiration is possibly exposed to redox regulation beyond known substrate-level effects. Additionally, our data support the view that 2-phosphoglycolate could be a key regulator of photosynthetic-photorespiratory metabolism as a whole.