Sugar beet hemoglobins: reactions with nitric oxide and nitrite reveal differential roles for nitrogen metabolism

Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris

Plant hemoglobins, often referred to as phytoglobins, play important roles in abiotic stress tolerance. Several essential small physiological metabolites can be bound to these heme proteins. In addition, phytoglobins can catalyze a range of different oxidative reactions in vivo. These proteins are often oligomeric, but the degree and relevance of subunit interactions are largely unknown. In this study, we delineate which residues are involved in dimer formation of a sugar beet phytoglobin type 1.2 (BvPgb1.2) using NMR relaxation experiments. E. coli cells harboring a phytoglobin expression vector were cultivated in isotope-labeled (²H, ¹³C and ¹⁵N) M9 medium. The triple-labeled protein was purified to homogeneity using two chromatographic steps. Two forms of BvPgb1.2 were examined, the oxy-form and the more stable cyanide-form. Using three-dimensional triple-resonance NMR experiments, sequence-specific assignments for CN-bound BvPgb1.2 were achieved for 137 backbone amide cross-peaks in the ¹H-¹⁵N TROSY spectrum, which amounts to 83% of the total number of 165 expected cross-peaks. A large proportion of the non-assigned residues are located in α-helixes G and H, which are proposed to be involved in protein dimerization. Such knowledge around dimer formation will be instrumental for developing a better understanding of phytoglobins' roles in planta.

Seeing through cells: Rapid measurement of intracellular target proteins

We have studied a method for making microbial cells transparent by immersing them in a solution with a high refractive index (RI). When the RI of the solution was matching that of the cells, light scattering was greatly diminished (by a factor of up to about 100) and the cell suspension became transparent, facilitating the spectrophotometric determination of intracellular compounds such as hemoglobin. We investigated the properties of several compounds such as sucrose, glycerol, bovine serum albumin, Ficoll^TM, and iodixanol (Optiprep^TM), each with advantages and disadvantages. Particularly good overall properties were found for iodixanol at a concentration of around 36% (w/v) and bovine serum albumin at a concentration of about 30% (w/v). By using this RI-matching principle the production of intracellular compounds can easily be followed in near real-time during fermentation processes. For example, some conditions for producing plant hemoglobin in Escherichia coli were conveniently determined without the need of any cell disintegration or product purification.

Oxidative Implications of Substituting a Conserved Cysteine Residue in Sugar Beet Phytoglobin BvPgb 1.2

Phytoglobins (Pgbs) are plant-originating heme proteins of the globin superfamily with varying degrees of hexacoordination. Pgbs have a conserved cysteine residue, the role of which is poorly understood. In this paper, we investigated the functional and structural role of cysteine in BvPgb1.2, a Class 1 Pgb from sugar beet (Beta vulgaris), by constructing an alanine-substituted mutant (Cys86Ala). The substitution had little impact on structure, dimerization, and heme loss as determined by X-ray crystallography, size-exclusion chromatography, and an apomyoglobin-based heme-loss assay, respectively. The substitution significantly affected other important biochemical properties. The autoxidation rate increased 16.7- and 14.4-fold for the mutant versus the native protein at 25 °C and 37 °C, respectively. Thermal stability similarly increased for the mutant by ~2.5 °C as measured by nano-differential scanning fluorimetry. Monitoring peroxidase activity over 7 days showed a 60% activity decrease in the native protein, from 33.7 to 20.2 U/mg protein. When comparing the two proteins, the mutant displayed a remarkable enzymatic stability as activity remained relatively constant throughout, albeit at a lower level, ~12 U/mg protein. This suggests that cysteine plays an important role in BvPgb1.2 function and stability, despite having seemingly little effect on its tertiary and quaternary structure.

Transcriptome profiling revealed candidate genes, pathways and transcription factors related to nitrogen utilization and excessive nitrogen stress in perennial ryegrass

Ryegrass (Lolium perenne L.), a high-quality forage grass, is a good nutrient source for herbivorous livestock. However, improving nitrogen use efficiency and avoiding nitrate toxicity caused by excessive nitrogen are continual challenges in ryegrass production. The molecular mechanism underlying the response of ryegrass to nitrogen, especially excessive nitrogen, remains unclear. In this study, the transcriptomic changes under different nitrogen levels were investigated in perennial ryegrass by high-throughput next-generation RNA sequencing. Phenotypic characterization showed that treatment with half of the standard N concentration (N0.5) led to a better growth state than the other three treatments. The treatments with the standard N concentration (N1) and treatments with ten times higher than the standard N concentration (N10) contained excessive nitrogen, which placed stress on plant growth. Analysis of differentially expressed genes indicated that 345 and 104 genes are involved in the regulation of nitrogen utilization and excessive nitrogen stress, respectively. KEGG enrichment analysis suggested that "photosynthesis-antenna proteins" may respond positively to appropriate nitrogen conditions, whereas "steroid biosynthesis", "carotenoid biosynthesis" and "C5-branched dibasic acid metabolism" were identified as the top significantly enriched pathways in response to excessive nitrogen. Additionally, 21 transcription factors (TFs) related to nitrogen utilization were classified into 10 families, especially the AP2-EREBP and MYB TF families. Four TFs related to excessive nitrogen stress were identified, including LOBs, NACs, AP2-EREBPs and HBs. The expression patterns of these selected genes were also analyzed. These results provide new insight into the regulatory mechanism of ryegrass in response to nitrogen utilization and excessive nitrogen stress.

Three classes of hemoglobins are required for optimal vegetative and reproductive growth of Lotus japonicus: genetic and biochemical characterization of LjGlb2-1

Legumes express two major types of hemoglobins, namely symbiotic (leghemoglobins) and non-symbiotic (phytoglobins), with the latter being categorized into three classes according to phylogeny and biochemistry. Using knockout mutants, we show that all three phytoglobin classes are required for optimal vegetative and reproductive development of Lotus japonicus. The mutants of two class 1 phytoglobins showed different phenotypes: Ljglb1-1 plants were smaller and had relatively more pods, whereas Ljglb1-2 plants had no distinctive vegetative phenotype and produced relatively fewer pods. Non-nodulated plants lacking LjGlb2-1 showed delayed growth and alterations in the leaf metabolome linked to amino acid processing, fermentative and respiratory pathways, and hormonal balance. The leaves of mutant plants accumulated salicylic acid and contained relatively less methyl jasmonic acid, suggesting crosstalk between LjGlb2-1 and the signaling pathways of both hormones. Based on the expression of LjGlb2-1 in leaves, the alterations of flowering and fruiting of nodulated Ljglb2-1 plants, the developmental and biochemical phenotypes of the mutant fed on ammonium nitrate, and the heme coordination and reactivity of the protein toward nitric oxide, we conclude that LjGlb2-1 is not a leghemoglobin but an unusual class 2 phytoglobin. For comparison, we have also characterized a close relative of LjGlb2-1 in Medicago truncatula, MtLb3, and conclude that this is an atypical leghemoglobin.

Improving Air Quality by Nitric Oxide Consumption of Climate-Resilient Trees Suitable for Urban Greening

Nitrogen oxides (NO_x), mainly a mixture of nitric oxide (NO) and nitrogen dioxide (NO₂), are formed by the reaction of nitrogen and oxygen compounds in the air as a result of combustion processes and traffic. Both deposit into leaves via stomata, which on the one hand benefits air quality and on the other hand provides an additional source of nitrogen for plants. In this study, we first determined the NO and NO₂ specific deposition velocities based on projected leaf area (sV _d) using a branch enclosure system. We studied four tree species that are regarded as suitable to be planted under predicted future urban climate conditions: Carpinus betulus, Fraxinus ornus, Fraxinus pennsylvanica and Ostrya carpinifolia. The NO and NO₂ sV_d were found similar in all tree species. Second, in order to confirm NO metabolization, we fumigated plants with ¹⁵NO and quantified the incorporation of ¹⁵N in leaf materials of these trees and four additional urban tree species (Celtis australis, Alnus spaethii, Alnus glutinosa, and Tilia henryana) under controlled environmental conditions. Based on these ¹⁵N-labeling experiments, A. glutinosa showed the most effective incorporation of ¹⁵NO. Third, we tried to elucidate the mechanism of metabolization. Therefore, we generated transgenic poplars overexpressing Arabidopsis thaliana phytoglobin 1 or 2. Phytoglobins are known to metabolize NO to nitrate in the presence of oxygen. The ¹⁵N uptake in phytoglobin-overexpressing poplars was significantly increased compared to wild-type trees, demonstrating that the NO uptake is enzymatically controlled besides stomatal dependence. In order to upscale the results and to investigate if a trade-off exists between air pollution removal and survival probability under future climate conditions, we have additionally carried out a modeling exercise of NO and NO₂ deposition for the area of central Berlin. If the actually dominant deciduous tree species (Acer platanoides, Tilia cordata, Fagus sylvatica, Quercus robur) would be replaced by the species suggested for future conditions, the total annual NO and NO₂ deposition in the modeled urban area would hardly change, indicating that the service of air pollution removal would not be degraded. These results may help selecting urban tree species in future greening programs.

Plant hemoglobins: a journey from unicellular green algae to vascular plants

Globins (Glbs) are widely distributed in archaea, bacteria and eukaryotes. They can be classified into proteins with 2/2 or 3/3 α-helical folding around the heme cavity. Both types of Glbs occur in green algae, bryophytes and vascular plants. The Glbs of angiosperms have been more intensively studied, and several protein structures have been solved. They can be hexacoordinate or pentacoordinate, depending on whether a histidine is coordinating or not at the sixth position of the iron atom. The 3/3 Glbs of class 1 and the 2/2 Glbs (also called class 3 in plants) are present in all angiosperms, whereas the 3/3 Glbs of class 2 have been only found in early angiosperms and eudicots. The three Glb classes are expected to play different roles. Class 1 Glbs are involved in hypoxia responses and modulate NO concentration, which may explain their roles in plant morphogenesis, hormone signaling, cell fate determination, nutrient deficiency, nitrogen metabolism and plant-microorganism symbioses. Symbiotic Glbs derive from class 1 or class 2 Glbs and transport O₂ in nodules. The physiological roles of class 2 and class 3 Glbs are poorly defined but could involve O₂ and NO transport and/or metabolism, respectively. More research is warranted on these intriguing proteins to determine their non-redundant functions.

A Plant Gene Encoding One-Heme and Two-Heme Hemoglobins With Extreme Reactivities Toward Diatomic Gases and Nitrite

In plants, symbiotic hemoglobins act as carriers and buffers of O₂ in nodules, whereas nonsymbiotic hemoglobins or phytoglobins (Glbs) are ubiquitous in tissues and may perform multiple, but still poorly defined, functions related to O₂ and/or nitric oxide (NO). Here, we have identified a Glb gene of the model legume Medicago truncatula with unique properties. The gene, designated MtGlb1-2, generates four alternative splice forms encoding Glbs with one or two heme domains and 215-351 amino acid residues. This is more than double the size of any hemoglobin from plants or other organisms described so far. A combination of molecular, cellular, biochemical, and biophysical methods was used to characterize these novel proteins. RNA-sequencing showed that the four splice variants are expressed in plant tissues. MtGlb1-2 is transcriptionally activated by hypoxia and its expression is further enhanced by an NO source. The gene is preferentially expressed in the meristems and vascular bundles of roots and nodules. Two of the proteins, bearing one or two hemes, were characterized using mutants in the distal histidines of the hemes. The Glbs are extremely reactive toward the physiological ligands O₂, NO, and nitrite. They show very high O₂ affinities, NO dioxygenase activity (in the presence of O₂), and nitrite reductase (NiR) activity (in the absence of O₂) compared with the hemoglobins from vertebrates and other plants. We propose that these Glbs act as either NO scavengers or NO producers depending on the O₂ tension in the plant tissue, being involved in the fast and fine tuning of NO concentration in the cytosol in response to sudden changes in O₂ availability.