Hypoxia Affects Nitrogen Uptake and Distribution in Young Poplar (Populus × canescens) Trees

Structure and Expression Analysis of PtrSUS, PtrINV, PtrHXK, PtrPGM, and PtrUGP Gene Families in Populus trichocarpa Torr. and Gray

Exogenous nitrogen and carbon can affect plant cell walls, which are composed of structural carbon. Sucrose synthase (SUS), invertase (INV), hexokinase (HXK), phosphoglucomutase (PGM), and UDP-glucose pyrophosphorylase (UGP) are the key enzymes of sucrose metabolism involved in cell wall synthesis. To understand whether these genes are regulated by carbon and nitrogen to participate in structural carbon biosynthesis, we performed genome-wide identification, analyzed their expression patterns under different carbon and nitrogen treatments, and conducted preliminary functional verification. Different concentrations of nitrogen and carbon were applied to poplar (Populus trichocarpa Torr. and Gray), which caused changes in cellulose, lignin, and hemicellulose contents. In poplar, 6 SUSs, 20 INVs, 6 HXKs, 4 PGMs, and 2 UGPs were identified. Moreover, the physicochemical properties, collinearity, and tissue specificity were analyzed. The correlation analysis showed that the expression levels of PtrSUS3/5, PtrNINV1/2/3/5/12, PtrCWINV3, PtrVINV2, PtrHXK5/6, PtrPGM1/2, and PtrUGP1 were positively correlated with the cellulose content. Meanwhile, the knockout of PtrNINV12 significantly reduced the cellulose content. This study could lay the foundation for revealing the functions of SUSs, INVs, HXKs, PGMs, and UGPs, which affected structural carbon synthesis regulated by nitrogen and carbon, proving that PtrNINV12 is involved in cell wall synthesis.

Physiological and comparative transcriptome analysis of the response and adaptation mechanism of the photosynthetic function of mulberry (Morus alba L.) leaves to flooding stress

Flooding has become one of the major abiotic stresses that seriously affects plant growth and development owing to changes in the global precipitation pattern. Mulberry (Morus alba L.) is a desirable tree spePhysocarpus amurensis Maxim andcies with high ecological and economic benefits. To reveal the response and adaptive mechanisms of the photosynthetic functions of mulberry leaves to flooding stress, chlorophyll synthesis, photosynthetic electron transfer and the Calvin cycle were investigated by physiological studies combined with an analysis of the transcriptome. Flooding stress inhibited the synthesis of chlorophyll (Chl) and decreased its content in mulberry leaves. The sensitivity of Chl a to flooding stress was higher than that of Chl b owing to the changes of CHLG (LOC21385082) and CAO (LOC21408165) that encode genes during chlorophyll synthesis. The levels of expression of Chl b reductase NYC (LOC112094996) and NYC (LOC21385774), which are involved in Chl b degradation, were upregulated on the fifteenth day of flooding, which accelerated the transformation of Chl b to Chl a, and upregulated the expression of PPH (LOC21385040) and PAO (LOC21395013). This accelerated the degradation of chlorophyll. Flooding stress significantly inhibited the photosynthetic function of mulberry leaves. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes under different days of flooding stress indicated significant enrichment in Photosynthesis-antenna proteins (map00196), Photosynthesis (map00195) and Carbon fixation in photosynthetic organisms (map00710). On the fifth day of flooding, 7 and 5 genes that encode antenna proteins were identified on LHCII and LHCI, respectively. They were significantly downregulated, and the degree of downregulation increased as the trees were flooded longer. Therefore, the power of the leaves to capture solar energy and transfer this energy to the reaction center was reduced. The chlorophyll fluorescence parameters and related changes in the expression of genes in the transcriptome indicated that the PSII and PSI of mulberry leaves were damaged, and their activities decreased under flooding stress. On the fifth day of flooding, electron transfer on the PSII acceptor side of mulberry leaves was blocked, and the oxygen-evolving complex (OEC) on the donor side was damaged. On the tenth day of flooding, the thylakoid membranes of mulberry leaves were damaged. Five of the six coding genes that mapped to the OEC were significantly downregulated. Simultaneously, other coding genes located at the PSII reaction center and those located at the PSI reaction center, including Cytb6/f, PC, Fd, FNR and ATP, were also significantly downregulated. In addition, the gas exchange parameters (P_n, G_s, T_r, and C_i) of the leaves decreased after 10 days of flooding stress primarily owing to the stomatal factor. However, on the fifteenth day of flooding, the value for the intracellular concentration of CO₂ was significantly higher than that on the tenth day of flooding. In addition, the differentially expressed genes identified in the Calvin cycle were significantly downregulated, suggesting that in addition to stomatal factors, non-stomatal factors were also important factors that mediated the decrease in the photosynthetic capacity of mulberry leaves. In conclusion, the inhibition of growth of mulberry plants caused by flooding stress was primarily related to the inhibition of chlorophyll synthesis, antenna proteins, photosynthetic electron transfer and the Calvin cycle. The results of this study provide a theoretical basis for the response and mechanism of adaptation of the photosynthetic function of mulberry to flooding stress.

Nitrate–Nitrite–Nitric Oxide Pathway: A Mechanism of Hypoxia and Anoxia Tolerance in Plants

Oxygen (O₂) is the most crucial substrate for numerous biochemical processes in plants. Its deprivation is a critical factor that affects plant growth and may lead to death if it lasts for a long time. However, various biotic and abiotic factors cause O₂ deprivation, leading to hypoxia and anoxia in plant tissues. To survive under hypoxia and/or anoxia, plants deploy various mechanisms such as fermentation paths, reactive oxygen species (ROS), reactive nitrogen species (RNS), antioxidant enzymes, aerenchyma, and adventitious root formation, while nitrate (NO₃⁻), nitrite (NO₂⁻), and nitric oxide (NO) have shown numerous beneficial roles through modulating these mechanisms. Therefore, in this review, we highlight the role of reductive pathways of NO formation which lessen the deleterious effects of oxidative damages and increase the adaptation capacity of plants during hypoxia and anoxia. Meanwhile, the overproduction of NO through reductive pathways during hypoxia and anoxia leads to cellular dysfunction and cell death. Thus, its scavenging or inhibition is equally important for plant survival. As plants are also reported to produce a potent greenhouse gas nitrous oxide (N₂O) when supplied with NO₃⁻ and NO₂⁻, resembling bacterial denitrification, its role during hypoxia and anoxia tolerance is discussed here. We point out that NO reduction to N₂O along with the phytoglobin-NO cycle could be the most important NO-scavenging mechanism that would reduce nitro-oxidative stress, thus enhancing plants’ survival during O₂-limited conditions. Hence, understanding the molecular mechanisms involved in reducing NO toxicity would not only provide insight into its role in plant physiology, but also address the uncertainties seen in the global N₂O budget.

Plants and water: the search for a comprehensive understanding

We learn early in life sciences classes that water is the solution of life, working in tandem with carbon to make life as we know it possible. Globally, the abundance of water can be misleading, as most of this water is unavailable, being overly salinized in the oceans or locked in deep underground reserves. On land, the critical supply is of freshwater, which is unevenly distributed in space and time. Even the wettest environments can experience episodic water deficit, and flash flooding periodically occurs in arid landscapes. While humanity can capture, store and transport freshwater over large distances to ensure sustained supply, such options are not apparent for plants except in an immediate local context. Plants must make do with the water in their immediate surroundings, whether it be abundant or scarce. How they do this has led to a myriad of adaptive solutions, involving capturing, storing and transporting water. The traits that enable them to optimize water use in a range of hydraulic environments, subject to multivariate selective constraints, are the essence of the discipline of plant-water relations.

Waterlogged Conditions Influence the Nitrogen, Phosphorus, Potassium, and Sugar Distribution in Sago Palm (Metroxylon sagu Rottb.) at Seedling Stages

Sago palm (Metroxylon sagu Rottb.) grows in well-drained mineral soil and in peatland with high groundwater levels until complete submersion. However, the published information on nutrient uptake and carbohydrate content in sago palms growing under waterlogging remains unreported. This experiment observed sago palm growth performance under normal soil conditions (non-submerged conditions) as a control plot and extended waterlogged conditions. Several parameters were analyzed: Plant morphological growth traits, nitrogen, phosphorus, potassium, and sugar concentration in the plant organ, including sucrose, glucose, starch, and non-structural carbohydrate. The analysis found that sago palm morphological growth traits were not significantly affected by extended waterlogging. However, waterlogging reduced carbohydrate levels in the upper part of the sago palm, especially the petiole, and increased sugar levels, especially glucose, in roots. Waterlogging also reduced N concentration in roots and leaflets and P in petioles. The K level was independent of waterlogging as the sago palm maintained a sufficient level in all of the plant organs. Long duration waterlogging may reduce the plant’s economic value as the starch level in the trunk decreases, although sago palm can grow while waterlogged.

Identification and expression analysis of the PtGATL genes under different nitrogen and carbon dioxide treatments in Populus trichocarpa

Pectin is one of the most important components of the plant cell wall. Galacturonosyltransferase-like (GATL) is an important enzyme involved in forming pectin in Arabidopsis thaliana. In this study, 12 PtGATL genes were identified and characterized based on the Populus trichocarpa genome using bioinformatics methods. The results showed that the PtGATLs contained four typical motifs, including DXD, LPPF, GLG, and HXXGXXKPW. According to phylogenetic analysis, PtGATLs were divided into six groups. Chromosome distribution and genome synteny analysis showed that there were 11 segmental-duplicated gene pairs with repeated fragments on chromosomes 2, 5, 7, 8, 10, and 14. Tissue-specific expression profiles indicated that these PtGATLs had different expression patterns. The transcription level of PtGATLs was regulated by different carbon dioxide and nitrogen concentrations. In conclusion, the identification and analysis of PtGATL genes in poplar provide important information on the gene function.

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The online version contains supplementary material available at 10.1007/s13205-022-03129-y.

Comparative transcriptomic analysis uncovers conserved pathways involved in adventitious root formation in poplar

Cutting propagation is widely used in establishing poplar plantations, and this approach requires efficient adventitious root (AR) forming capacities. Although poplar species are considered to form roots easily, interspecific variations in AR formation are still observed. To better understand the gene regulatory network underlying the conserved modified pathways that are essential for AR formation in poplar species, comparative transcriptomic approaches were applied to identify the conserved common genes that were differentially expressed during the AR formation processes in two poplar species (Populus × euramericana and P. simonii) in woody plant medium (WPM). A total of 2146 genes were identified as conserved genes that shared similar gene expression profiles in at least one comparison. These conserved genes were enriched in diverse hormone signaling pathways, as well as the mitogen-associated protein kinase (MAPK) signaling pathway, suggesting an important role for signaling transduction in coordinating external stimuli and endogenous physiological status during AR regulation in poplar. Furthermore, the co-expression network analysis of conserved genes allowed identification of several co-expressed modules (CM) that are co-expressed with distinct biological functions, for instance, CM1 was enriched in defense response and hormone signaling, CM2 and CM3 were overrepresented in defense response-related pathways and for cell cycle, respectively. These results suggest that the AR formation processes in poplar were finely tuned at the transcriptomic level by integrating multiple biological processes essential for AR formation. Our results suggest conserved machinery for AR formation in poplar and generated informative gene co-expression networks that describe the basis of AR formation in these species.

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The online version contains supplementary material available at 10.1007/s12298-021-01054-7.

The hypoxia-reoxygenation stress in plants

Plants are very plastic in adapting growth and development to changing adverse environmental conditions. This feature will be essential for plants to survive climate changes characterized by extreme temperatures and rainfall. Although plants require molecular oxygen (O2) to live, they can overcome transient low-O2 conditions (hypoxia) until return to standard 21% O2 atmospheric conditions (normoxia). After heavy rainfall, submerged plants in flooded lands undergo transient hypoxia until water recedes and normoxia is recovered. The accumulated information on the physiological and molecular events occurring during the hypoxia phase contrasts with the limited knowledge on the reoxygenation process after hypoxia, which has often been overlooked in many studies in plants. Phenotypic alterations during recovery are due to potentiated oxidative stress generated by simultaneous reoxygenation and reillumination leading to cell damage. Besides processes such as N-degron proteolytic pathway-mediated O2 sensing, or mitochondria-driven metabolic alterations, other molecular events controlling gene expression have been recently proposed as key regulators of hypoxia and reoxygenation. RNA regulatory functions, chromatin remodeling, protein synthesis, and post-translational modifications must all be studied in depth in the coming years to improve our knowledge on hypoxia-reoxygenation transition in plants, a topic with relevance in agricultural biotechnology in the context of global climate change.

Bioinformatics analysis of PAE family in Populus trichocarpa and responsiveness to carbon and nitrogen treatment

Plant Pectin acetylesterase (PAE) belongs to family CE13 of carbohydrate esterases in the CAZy database. The ability of PAE to regulate the degree of acetylation of pectin, an important polysaccharide in the cell wall, affects the structure of plant cell wall. In this study, ten PtPAE genes were identified and characterized in Populus trichocarpa genome using bioinformatics methods, and the physiochemical properties such as molecular weight, isoelectric points, and hydrophilicity, as well as the secondary and tertiary structure of the protein were predicted. According to phylogenetic analysis, ten PtPAEs can be divided into three evolutionary clades, each of which had similar gene structure and motifs. Tissue-specific expression profiles indicated that the PtPAEs had different expression patterns. Real-time quantitative PCR (RT-qPCR) analysis showed that transcription level of PtPAEs was regulated by different CO₂ and nitrogen concentrations. These results provide important information for the study of the phylogenetic relationship and function of PtPAEs in Populus trichocarpa.

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The online version contains supplementary material available at 10.1007/s13205-021-02918-1.

Circadian patterns of xylem sap properties and their covariation with plant hydraulic traits in hybrid aspen

Physiological processes taking place in plants are subject to diverse circadian patterns but some of them are poorly documented in natural conditions. The daily dynamics of physico-chemical properties of xylem sap and their covariation with tree hydraulic traits were investigated in hybrid aspen (Populus tremula L.×P. tremuloides Michx) in field conditions in order to clarify which environmental drivers govern the daily variation in these parameters. K⁺ concentration ([K⁺]), electrical conductivity (σ_sap), osmolality (Osm) and pH of the xylem sap, as well as branch hydraulic traits, were measured in the field over 24-h cycles. All studied xylem sap properties and hydraulic characteristics including whole-branch (K_wb), leaf blade (K_lb) and petiole hydraulic conductances (K_P) showed clear daily dynamics. Air temperature (T_A) and photosynthetic photon flux density (PPFD), but also water vapour pressure deficit (VPD) and relative humidity (RH), had significant impacts on K_wbK_lb, K_P, [K⁺] and σ_sap. Osm varied only with light intensity, while K_B varied depending on atmospheric evaporative demand expressed as T_A, VPD or RH. Xylem sap pH depended inversely on soil water potential (Ψ_S) and during daylight also on VPD. Although soil water content was close to saturation during the study period, Ψ_S influenced also [K⁺] and σ_sap. The present study presents evidence of coupling between circadian patterns of xylem sap properties and plant hydraulic conductance providing adequate water supply to foliage under environmental conditions characterised by diurnal variation.