Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves

A dynamic phosphoproteomic analysis provides insight into the C4 plant maize (Zea mays L.) response to natural diurnal changes

As sessile organisms, plants need to respond to rapid changes in numerous environmental factors, mainly diurnal changes of light, temperature, and humidity. Maize is the world's most grown crop, and as a C4 plant it exhibits high photosynthesis capacity, reaching the highest rate of net photosynthesis at midday; that is, there is no "midday depression." Revealing the physiological responses to diurnal changes and underlying mechanisms will be of great significance for guiding maize improvement efforts. In this study, we collected maize leaf samples and analyzed the proteome and phosphoproteome at nine time points during a single day/night cycle, quantifying 7424 proteins and 5361 phosphosites. The new phosphosites identified in our study increased the total maize phosphoproteome coverage by 8.5%. Kinase-substrate network analysis indicated that 997 potential substrates were phosphorylated by 20 activated kinases. Through analysis of proteins with significant changes in abundance and phosphorylation, we found that the response to a heat stimulus involves a change in the abundance of numerous proteins. By contrast, the high light at noon and rapidly changing light conditions induced changes in the phosphorylation level of proteins involved in processes such as chloroplast movement, photosynthesis, and C4 pathways. Phosphorylation is involved in regulating the activity of large number of enzymes; for example, phosphorylation of S55 significantly enhanced the activity of maize phosphoenolpyruvate carboxykinase1 (ZmPEPCK1). Overall, the database of dynamic protein abundance and phosphorylation we have generated provides a resource for the improvement of C4 crop plants.

Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon

Lignin biosynthesis begins with the deamination of phenylalanine and tyrosine (Tyr) as a key branch point between primary and secondary metabolism in land plants. Here, we used a systems biology approach to investigate the global metabolic responses to lignin pathway perturbations in the model grass Brachypodium distachyon. We identified the lignin biosynthetic protein families and found that ammonia-lyases (ALs) are among the most abundant proteins in lignifying tissues in grasses. Integrated metabolomic and proteomic data support a link between lignin biosynthesis and primary metabolism mediated by the ammonia released from ALs that is recycled for the synthesis of amino acids via glutamine. RNA interference knockdown of lignin genes confirmed that the route of the canonical pathway using shikimate ester intermediates is not essential for lignin formation in Brachypodium, and there is an alternative pathway from Tyr via sinapic acid for the synthesis of syringyl lignin involving yet uncharacterized enzymatic steps. Our findings support a model in which plant ALs play a central role in coordinating the allocation of carbon for lignin synthesis and the nitrogen available for plant growth. Collectively, these data also emphasize the value of integrative multiomic analyses to advance our understanding of plant metabolism.

Physiological and proteomic analyses revealed the response mechanisms of two different drought-resistant maize varieties

BACKGROUND

Drought stress severely limits maize seedling growth and crop yield. Previous studies have elucidated the mechanisms by which maize acquires drought resistance and contends with water deficiency. However, the link between the physiological and molecular variations among maize cultivars are unknown. Here, physiological and proteomic analyses were conducted to compare the stress responses of two maize cultivars with contrasting drought stress tolerance.

RESULTS

The physiological analysis showed that the drought-tolerant SD609 maize variety maintains relatively high photochemical efficiency by enhancing its protective cyclic electron flow (CEF) mechanism and antioxidative enzymes activities. Proteomics analysis revealed that 198 and 102 proteins were differentially expressed in SD609 and the drought-sensitive SD902 cultivar, respectively. GO and KEGG enrichments indicated that SD609 upregulated proteins associated with photosynthesis, antioxidants/detoxifying enzymes, molecular chaperones and metabolic enzymes. Upregulation of the proteins related to PSII repair and photoprotection improved photochemical capacity in SD609 subjected to moderate drought stress. In SD902, however, only the molecular chaperones and sucrose synthesis pathways were induced and they failed to protect the impaired photosystem. Further analysis demonstrated that proteins related to the electron transport chain (ETC) and redox homeostasis as well as heat shock proteins (HSPs) may be important in protecting plants from drought stress.

CONCLUSIONS

Our experiments explored the mechanism of drought tolerance and clarified the interconnections between the physiological and proteomic factors contributing to it. In summary, our findings aid in further understanding of the drought tolerance mechanisms in maize.

Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis

Heterosis or hybrid vigor is widespread in plants and animals. Although the molecular basis for heterosis has been extensively studied, metabolic and proteomic contributions to heterosis remain elusive. Here we report an integrative analysis of time-series metabolome and proteome data in maize (Zea mays) hybrids and their inbred parents. Many maize metabolites and proteins are diurnally regulated, and many of these show nonadditive abundance in the hybrids, including key enzymes and metabolites involved in carbon assimilation. Compared with robust trait heterosis, metabolic heterosis is relatively mild. Interestingly, most amino acids display negative mid-parent heterosis (MPH), i.e., having lower values than the average of the parents, while sugars, alcohols, and nucleoside metabolites show positive MPH. From the network perspective, metabolites in the photosynthetic pathway show positive MPH, whereas metabolites in the photorespiratory pathway show negative MPH, which corresponds to nonadditive protein abundance and enzyme activities of key enzymes in the respective pathways in the hybrids. Moreover, diurnally expressed proteins that are upregulated in the hybrids are enriched in photosynthesis-related gene-ontology terms. Hybrids may more effectively remove toxic metabolites generated during photorespiration, and thus maintain higher photosynthetic efficiency. These metabolic and proteomic resources provide unique insight into heterosis and its utilization for high yielding maize and other crop plants.

Comparative physiological and transcriptomic analysis of pear leaves under distinct training systems

Canopy architecture is critical in determining the light interception and distribution, and subsequently the photosynthetic efficiency and productivity. However, the physiological responses and molecular mechanisms by which pear canopy architectural traits impact on photosynthesis remain poorly understood. Here, physiological investigations coupled with comparative transcriptomic analyses were performed in pear leaves under distinct training systems. Compared with traditional freestanding system, flat-type trellis system (DP) showed higher net photosynthetic rate (P_N) levels at the most time points throughout the entire monitored period, especially for the interior of the canopy in sunny side. Gene ontology analysis revealed that photosynthesis, carbohydrate derivative catabolic process and fatty acid metabolic process were over-represented in leaves of DP system with open-canopy characteristics. Weighted gene co-expression network analysis uncovered a significant network module positive correlated with P_N value. The hub genes (PpFKF1 and PpPRR5) of the module were enriched in circadian rhythm pathway, suggesting a functional role for circadian clock genes in mediating photosynthetic performance under distinct training systems. These results draw a link between pear photosynthetic response and specific canopy architectural traits, and highlight light harvesting and circadian clock network as potential targets for the input signals from the fluctuating light availability under distinct training systems.

CO2 uptake and chlorophyll a fluorescence of Suaeda fruticosa grown under diurnal rhythm and after transfer to continuous dark

Although only 2-4% of absorbed light is emitted as chlorophyll (Chl) a fluorescence, its measurement provides valuable information on photosynthesis of the plant, particularly of Photosystem II (PSII) and Photosystem I (PSI). In this paper, we have examined photosynthetic parameters of Suaeda fruticosa L. (family: Amaranthaceae), surviving under extreme xerohalophytic conditions, as influenced by diurnal rhythm or continuous dark condition. We report here CO₂ gas exchange and the kinetics of Chl a fluorescence of S. fruticosa, made every 3 hours (hrs) for 3 days, using a portable infra-red gas analyzer and a Handy PEA fluorimeter. Our measurements on CO₂ gas exchange show the maximum rate of photosynthesis to be at 08:00 hrs under diurnal condition and at 05:00 hrs under continuous dark. From the OJIP phase of Chl a fluorescence transient, we have inferred that the maximum quantum yield of PSII photochemistry must have increased during the night under diurnal rhythm, and between 11:00 and 17:00 hrs under constant dark. Overall, our study has revealed novel insights into how photosynthetic reactions are affected by the photoperiodic cycles in S. fruticosa under high salinity. This study has further revealed a unique strategy operating in this xero-halophyte where the repair mechanism for damaged PSII operates during the dark, which, we suggest, contributes to its ecological adaptation and ability to survive and reproduce under extreme saline, high light, and drought conditions. We expect these investigations to help in identifying key genes and pathways for raising crops for saline and dry areas.

Leaf Temperature and Vapour Pressure Deficit (VPD) Driving Stomatal Conductance and Biochemical Processes of Leaf Photosynthetic Rate in a Subtropical Evergreen Coniferous Plantation

Photosynthesis is arguably the most important biochemical process on Earth, which is dramatically influenced by environmental conditions. How environmental factors drive stomatal conductance and biochemical processes of leaf photosynthetic rate has not been sufficiently investigated in subtropical China. In this study, we analysed the effects of stomatal and biochemical parameters on the photosynthetic rate of native Masson’s pine (Pinus massoniana Lamb.) and exotic slash pine (Pinus elliottii Engelm.) in response to leaf temperature and vapour pressure deficit (VPD) in subtropical China, based on leaf gas exchange measurements in 2016. Our results showed that there was no significant difference in the light-saturated photosynthetic rate (Asat) between native Masson’s pine and exotic slash pine. The seasonal patterns of maximum rate of the carboxylation (Vcmax25) were basically consistent with seasonal patterns of Asat for both species. The positive effect of leaf temperature on Asat was mainly produced through its positive effect on Vcmax25. Leaf temperature had no significant effect on stomatal conductance. Vcmax25 and gs simultaneously affected Asat in response to VPD. Our results highlighted the importance of biochemical processes in limiting leaf photosynthetic rate in response to environmental conditions in subtropical evergreen coniferous plantations.