Integrated operation of the photorespiratory cycle and cytosolic metabolism in the modulation of primary nitrogen assimilation and export of organic N-transport compounds from leaves: a hypothesis

Identification and expression pattern analysis of PtCarA and PtCarB genes in Populus trichocarpa under different nitrogen treatments

Carbamoyl phosphate synthetase (CPS) catalyses the synthesis of ammonia carbamoyl phosphate (CP), which plays a key role in the biosynthesis of arginine and pyrimidine nucleotides. There are two subunits of the CPS enzyme in Populus trichocarpa, CarA (small subunit) and CarB (large subunit). Only when they coexist can CPS catalyse synthesis of CP. However, it is not clear how CPS responds to nitrogen (N) to affect arginine and pyrimidine nucleotide biosynthesis. In this study, bioinformatics methods were used to analyse the expression patterns of genes encoding CarA and CarB, and qRT-PCR and RNA-seq were used to investigate their molecular responses under different N concentrations. Phylogenetic analysis revealed that the phylogenetic trees of CarA and CarB had similar topologies. qRT-PCR showed that the PtCarA and PtCarB genes were regulated by N, while their N-regulated patterns differed in different tissues. The expression patterns of PtCarA and PtCarB show a significant positive correlation according to qRT-PCR and RNA-seq. The analysis of promoter cis-acting elements showed that the promoter regions of PtCarA1, PtCarA2 and PtCarB contained some identical cis-acting elements. According to analysis of the phylogenetic tree, expression patterns and promoter elements, we speculate that there might be coevolution among PtCarA1, PtCarA2 and PtCarB. This study provides valuable information for further understanding the function of CPS in poplar, especially for N response, and provides new ideas for studying the evolution of gene families related to heteromultimers.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

Nitrogen sources and CO2 concentration synergistically affect the growth and metabolism of tobacco plants

The initial stimulation of photosynthesis under elevated CO2 concentrations (eCO2) is often followed by a decline in photosynthesis, known as CO2 acclimation. Changes in N levels under eCO2 can have different effects in plants fertilized with nitrate (NO3-) or ammonium (NH4+) as the N source. NO3- assimilation consumes approximately 25% of the energy produced by an expanded leaf, whereas NH4+ requires less energy to be incorporated into organic compounds. Although plant-N interactions are important for the productivity and nutritional value of food crops worldwide, most studies have not compared the performance of plants supplied with different forms of N. Therefore, this study aims to go beyond treating N as the total N in the soil or the plant because the specific N compounds formed from the available N forms become highly engaged in all aspects of plant metabolism. To this end, plant N metabolism was analyzed through an experiment with eCO2 and fertigation with NO3- and/or NH4+ as N sources for tobacco (Nicotiana tabacum) plants. The results showed that the plants that received only NO3- as a source of N grew more slowly when exposed to a CO2 concentration of 760 μmol mol-1 than when they were exposed to ambient CO2 conditions. On the other hand, in plants fertigated with only NH4+, eCO2 enhanced photosynthesis. This was essential for the maintenance of the metabolic pathways responsible for N assimilation and distribution in growing tissues. These data show that the physiological performance of tobacco plants exposed to eCO2 depends on the form of inorganic N that is absorbed and assimilated.

Daring metabolic designs for enhanced plant carbon fixation

Increasing agricultural productivity is one of the major challenges our society faces. While multiple strategies to enhance plant carbon fixation have been suggested, and partially implemented, most of them are restricted to relatively simple modifications of endogenous metabolism, i.e., "low hanging fruit". Here, I portray the next generation of metabolic solutions to increase carbon fixation rate and yield. These strategies involve major rewiring of central metabolism, including dividing Rubisco's catalysis between several enzymes, replacing Rubisco with a different carboxylation reaction, substituting the Calvin Cycle with alternative carbon fixation pathways, and engineering photorespiration bypass routes that do not release carbon. While the barriers for implementing these elaborated metabolic architectures are quite significant, if we truly want to revolutionize carbon fixation, only daring engineering efforts will lead the way.

Plants increase CO2 uptake by assimilating nitrogen via the photorespiratory pathway

Photorespiration is a major bioengineering target for increasing crop yields as it is often considered a wasteful process. Photorespiratory metabolism is integrated into leaf metabolism and thus may have certain benefits. Here, we show that plants can increase their rate of photosynthetic CO₂ uptake when assimilating nitrogen de novo via the photorespiratory pathway by fixing carbon as amino acids in addition to carbohydrates. Plants fed NO₃^- had higher rates of CO₂ assimilation under photorespiratory than low-photorespiratory conditions, while plants lacking NO₃^- nutrition exhibited lower stimulation of CO₂ uptake. We modified the widely used Farquhar, von Caemmerer and Berry photosynthesis model to include the carbon and electron requirements for nitrogen assimilation via the photorespiratory pathway. Our modified model improves predictions of photosynthetic CO₂ uptake and of rates of photosynthetic electron transport. The results highlight how photorespiration can improve photosynthetic performance despite reducing the efficiency of Rubisco carboxylation.

Expression and properties of the glyoxysomal and cytosolic forms of isocitrate lyase in Amaranthus caudatus L

Isocitrate lyase (EC 4.1.3.1) catalyzes the reversible conversion of d-isocitrate to succinate and glyoxylate. It is usually associated with the glyoxylate cycle in glyoxysomes, although the non-glyoxysomal form has been reported and its relation to interconversion of organic acids outside the glyoxylate cycle suggested. We investigated the expression of two isocitrate lyase genes and activities of the glyoxysomal (ICL1) and cytosolic (ICL2) forms of isocitrate lyase in amaranth (Amaranthus caudatus L.) seedlings. Both forms were separated and purified. The cytosolic form had a low optimum pH (6.5) and was activated by Mn(2+) ions, while Mg(2+) was ineffective, and had a lower affinity to d, l-isocitrate (Km 63 μM) as compared to the glyoxysomal form (optimum pH 7.5, K(m) 45 μM), which was activated by Mg(2+). The highest ICL1 activity was observed on the 3rd day of germination; then the activity and expression of the corresponding gene decreased, while the activity of ICL2 and gene expression increased to the 7th day of germination and then remained at the same level. It is concluded that the function of ICL1 is related to the glyoxylate cycle while ICL2 functions independently from the glyoxylate cycle and interconverts organic acids in the cytosol.

Comparative proteomic analysis of early salt stress responsive proteins in roots and leaves of rice

Growth and productivity of rice (Oryza sativa L.) are severely affected by salinity. Understanding the mechanisms that protect rice and other important cereal crops from salt stress will help in the development of salt-stress-tolerant strains. In this study, rice seedlings of the same genetic species with various salt tolerances were studied. We first used 2DE to resolve the expressed proteome in rice roots and leaves and then used nanospray liquid chromatography/tandem mass spectrometry to identify the differentially expressed proteins in rice seedlings after salt treatment. The 2DE assays revealed that there were 104 differentially expressed protein spots in rice roots and 59 in leaves. Then, we identified 83 proteins in rice roots and 61 proteins in rice leaves by MS analysis. Functional classification analysis revealed that the differentially expressed proteins from roots could be classified into 18 functional categories while those from leaves could be classified into 11 functional categories. The proteins from rice seedlings that most significantly contributed to a protective effect against increased salinity were cysteine synthase, adenosine triphosphate synthase, quercetin 3-O-methyltransferase 1, and lipoxygenase 2. Further analysis demonstrated that the primary mechanisms underlying the ability of rice seedlings to tolerate salt stress were glycolysis, purine metabolism, and photosynthesis. Thus, we suggest that differentially expressed proteins may serve as marker group for the salt tolerance of rice.