NCPbook: a comprehensive database of non-canonical peptides.

Non-canonical peptides (NCPs) are a class of peptides generated from regions previously thought of as non-coding, such as introns, 5' untranslated regions (UTRs), 3' UTRs, and intergenic regions. In recent years, the significance and diverse functions of NCPs have come to light, yet a systematic and comprehensive NCP database remains absent. Here, we developed NCPbook (https://ncp.wiki/ncpbook/), a database of evidence-supported NCPs, which aims to provide a resource for efficient exploration, analysis, and manipulation of NCPs. NCPbook incorporates data from diverse public databases and scientific literature. The current version of NCPbook includes 180,676 NCPs across 29 different species, evidenced by mass spectrometry (MS), ribosome profiling (Ribo-seq), or molecular experiments (ME). These NCPs are distributed across kingdoms, comprising 123,408 from 14 plant species, 56,999 from seven animal species, and 269 from eight microbial species. Furthermore, NCPbook encompasses 9,166 functionally characterized NCPs playing important roles in immunity, stress resistance, growth, and development. Equipped with a user-friendly interface, NCPbook allows users to search, browse, visualize, and retrieve data, making it an indispensable platform for researching NCPs in various plant, animal, and microbial species.

Matrix stiffness-dependent STEAP3 coordinated with PD-L2 identify tumor responding to sorafenib treatment in hepatocellular carcinoma.

BACKGROUND: Ferroptosis have been implicated in tumorigenesis, tumor progression, and chemo- and immuno-therapy in cirrhotic hepatocellular carcinoma (HCC), indicating its association with matrix stiffness and clinical benefit of targeting drugs or immune checkpoint inhibitor. Here, we postulated that increased matrix stiffness reduces ferroptosis and impairs tumor immunity by regulating the expression of ferroptosis- and immune-related genes in HCC, which might be a robust predictor of therapeutic efficacy. METHODS: Using publicly available tissue microarray datasets, liver cancer rat model, and clinical specimen, ferroptosis-related differential genes in HCV-infected cirrhotic HCC and its mechanical heterogeneous pattern of expression were screened and identified. Further investigation on the underlying mechanism of matrix stiffness-regulated ferroptosis and the expression of immune mediator were performed. Finally, threshold analysis of HCC cases with sorafenib treatment revealed the value of clinical applications of these potential predictors. RESULTS: STEAP3 was identified as the ferroptosis-related differential genes in HCV-infected cirrhotic HCC. Stiffer matrix decreased STEAP3 in the invasive front area of HCC and the liver cirrhotic tissue. Contrarily, softer matrix induced STEAP3 in the central area of HCC and the normal liver tissue. Immunological correlation of STEAP3 in cirrhotic HCC showed that STEAP3-mediated immune infiltration of CD4+ T and CD8+ T cells, macrophages, neutrophils, and dendritic cells and HCC prognosis, predicting to regulate immune infiltration. Overexpression of STEAP3 induced ferroptosis and inhibited the expression of immune mediator of PD-L2 on a stiff matrix. Especially, the ferroptosis- and immune-related gene predictive biomarker (FIGPB), including STEAP3 and PD-L2, predicts better clinical benefit of sorafenib in HCC patients. CONCLUSIONS: This finding identifies matrix stiffness impairs ferroptosis and anti-tumor immunity by mediating STEAP3 and PD-L2. More importantly, coordinated with PD-L2, matrix stiffness-dependent STEAP3 could be applied as the independent predictors to favorable sorafenib response, and thus targeting it could be a potential diagnosis and treatment strategy for HCC.

Demethylzeylasteral targets lactate by inhibiting histone lactylation to suppress the tumorigenicity of liver cancer stem cells.

Cancer stem cells drive tumor initiation, progression, and recurrence, which compromise the effectiveness of anti-tumor drugs. Here, we report that demethylzeylasteral (DML), a triterpene anti-tumor compound, suppressed tumorigenesis of liver cancer stem cells (LCSCs) by interfering with lactylation of a metabolic stress-related histone. Using RNA sequencing (RNA-seq) and gas chromatography-mass spectrometric (GC-MS) analysis, we showed that the glycolysis metabolic pathway contributed to the anti-tumor effects of DML, and then focused on lactate downstream regulation as the molecular target. Mechanistically, DML opposed the progress of hepatocellular carcinoma (HCC), which was efficiently facilitated by the increase in H3 histone lactylation. Two histone modification sites: H3K9la and H3K56la, which were found to promote tumorigenesis, were inhibited by DML. In addition, we used a nude mouse tumor xenograft model to confirm that the anti-liver cancer effects of DML are mediated by regulating H3 lactylation in vivo. Our findings demonstrate that DML suppresses the tumorigenicity induced by LCSCs by inhibiting H3 histone lactylation, thus implicating DML as a potential candidate for the supplementary treatment of hepatocellular carcinoma.

Ascorbate peroxidase 1 confers resistance to southern corn leaf blight in maize.

Southern corn leaf blight (SCLB), caused by Bipolaris maydis, is one of the most devastating diseases affecting maize production. However, only one SLCB resistance gene, conferring partial resistance, is currently known, underscoring the importance of isolating new SCLB resistance-related genes. Here, we performed a comparative proteomic analysis and identified 258 proteins showing differential abundance during the maize response to B. maydis. These proteins included an ascorbate peroxidase (Zea mays ascorbate peroxidase 1 (ZmAPX1)) encoded by a gene located within the mapping interval of a previously identified quantitative trait locus associated with SCLB resistance. ZmAPX1 overexpression resulted in lower H2 O2 accumulation and enhanced resistance against B. maydis. Jasmonic acid (JA) contents and transcript levels for JA biosynthesis and responsive genes increased in ZmAPX1-overexpressing plants infected with B. maydis, whereas Zmapx1 mutants showed the opposite effects. We further determined that low levels of H2 O2 are accompanied by an accumulation of JA that enhances SCLB resistance. These results demonstrate that ZmAPX1 positively regulates SCLB resistance by decreasing H2 O2 accumulation and activating the JA-mediated defense signaling pathway. This study identified ZmAPX1 as a potentially useful gene for increasing SCLB resistance. Furthermore, the generated data may be relevant for clarifying the functions of plant APXs.

Large-scale reconstruction of chromatin structures of maize temperate and tropical inbred lines.

Maize is a model plant species often used for genetics and genomics research because of its genetic diversity. There are prominent morphological, genetic, and epigenetic variations between tropical and temperate maize lines. However, the genome-wide chromatin conformations of these two maize types remain unexplored. We applied a Hi-C approach to compare the genome-wide chromatin interactions between temperate inbred line D132 and tropical line CML288. A reconstructed maize three-dimensional genome model revealed the spatial segregation of the global A and B compartments. The A compartments contain enriched genes and active epigenome marks, whereas the B compartments are gene-poor, transcriptionally silent chromatin regions. Whole-genome analyses indicated that the global A compartment content of CML288 was 3.12% lower than that of D132. Additionally, global and A/B sub-compartments were associated with differential gene expression and epigenetic changes between two inbred lines. About 25.3% of topologically associating domains (TADs) were determined to be associated with complex domain-level modifications that induced transcriptional changes, indicative of a large-scale reorganization of chromatin structures between the inbred maize lines. Furthermore, differences in chromatin interactions between the two lines correlated with epigenetic changes. These findings provide a solid foundation for the wider plant community to further investigate the genome-wide chromatin structures in other plant species.

Comprehensive dynamic transcriptome analysis at two seed germination stages in maize (Zea mays L.).

Seed germination, as an integral stage of crop production, directly affects Zea mays (maize) yield and grain quality. However, the molecular mechanisms of seed germination remain unclear in maize. We performed comparative transcriptome analysis of two maize inbred lines, Yu82 and Yu537A, at two stages of seed germination. Expression profile analysis during seed germination revealed that a total of 3381 and 4560 differentially expressed genes (DEGs) were identified in Yu82 and Yu537A at the two stages. Transcription factors were detected from several families, such as the bZIP, ERF, WRKY, MYB and bHLH families, which indicated that these transcription factor families might be involved in driving seed germination in maize. Prominent DEGs were submitted for KEGG enrichment analysis, which included plant hormones, amino acid mechanism, nutrient reservoir, metabolic pathways and ribosome. Of these pathways, genes associated with plant hormones, especially gibberellins, abscisic acid and auxin may be important for early germination in Yu82. In addition, DEGs involved in amino acid mechanism showed significantly higher expression levels in Yu82 than in Yu537A, which indicated that energy supply from soluble sugars and amino acid metabolism may contribute to early germination in Yu82. This results provide novel insights into transcriptional changes and gene interactions in maize during seed germination.

Comparative proteomics combined with analyses of transgenic plants reveal ZmREM1.3 mediates maize resistance to southern corn rust.

Southern corn rust (SCR), which is a destructive disease caused by Puccinia polysora Underw. (P. polysora), commonly occurs in warm-temperate and tropical regions. To identify candidate proteins related to SCR resistance and characterize the molecular mechanisms underlying the maize-P. polysora interaction, a comparative proteomic analysis of susceptible and resistant maize lines was performed. Statistical analyses revealed 1489 differentially abundant proteins in the resistant line, as well as 1035 differentially abundant proteins in the susceptible line. After the P. polysora infection, the abundance of one remorin protein (ZmREM1.3) increased in the resistant genotype, but decreased in the susceptible genotype. Plant-specific remorins are important for responses to microbial infections as well as plant signalling processes. In this study, transgenic maize plants overexpressing ZmREM1.3 exhibited enhanced resistance to the biotrophic P. polysora. In contrast, homozygous ZmREM1.3 UniformMu mutant plants were significantly more susceptible to P. polysora than wild-type plants. Additionally, the ZmREM1.3-overexpressing plants accumulated more salicylic acid (SA) and jasmonic acid (JA). Moreover, the expression levels of defence-related genes were higher in ZmREM1.3-overexpressing maize plants than in non-transgenic control plants in response to the P. polysora infection. Overall, our results provide evidence that ZmREM1.3 positively regulates maize defences against P. polysora likely via SA/JA-mediated defence signalling pathways. This study represents the first large-scale proteomic analysis of the molecular mechanisms underlying the maize-P. polysora interaction. This is also the first report confirming the remorin protein family affects plant resistance to SCR.

MicroRNA 399 as a potential integrator of photo-response, phosphate homeostasis, and sucrose signaling under long day condition.

BACKGROUND: Photoperiod-sensitivity is a critical endogenous regulatory mechanism for plant growth and development under specific environmental conditions, while phosphate and sucrose signaling processes play key roles in cell growth and organ initiation. MicroRNA399 is phosphate-responsive, but, whether it has roles in other metabolic processes remains unknown. RESULTS: MicroRNA399 was determined to be sucrose-responsive through a microRNA array assay. High levels of sucrose inhibited the accumulation of microRNA399 family under phosphate starvation conditions in Arabidopsis thaliana. Similarly, exogenous sucrose supplementation also reduced microRNA399 expression in maize at developmental transition stages. RNA sequencing of a near-isogenic line(photoperiod-sensitive) line and its recurrent parent Huangzao4, a photoperiod-insensitive line, was conducted at various developmental stages. Members of microRNA399 family were down-regulated under long-day conditions in the photoperiod-sensitive near-isogenic line that accumulated more sucrose in vivo compared with the control line Huangzao4. CONCLUSION: MicroRNA399s may play central roles in the integration of sucrose sensing and photoperiodic responses under long day conditions in maize.

Condensed Tannins Affect Bacterial and Fungal Microbiomes and Mycotoxin Production during Ensiling and upon Aerobic Exposure.

Purple prairie clover (PPC; Dalea purpurea Vent.) containing 84.5 g/kg dry matter (DM) of condensed tannin (CT) was ensiled without (control) or with polyethylene glycol (PEG) for 76 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics were determined, and the composition of bacterial and fungal communities were assessed using metagenomic sequencing. The addition of polyethylene glycol (PEG) that deactivated CT at ensiling increased (P < 0.05 to ∼0.001) soluble N, nonprotein N, lactic acid, total volatile fatty acids, ammonia N, deoxynivalenol (DON), and ochratoxin A (OTA) but decreased (P < 0.001) pH and water-soluble carbohydrates. The concentrations of DON and OTA increased (P < 0.001) for both silages, with the extent of increase being greater for control than for PEG-treated silage during aerobic exposure. The PEG-treated silage exhibited higher (P < 0.01 to ∼0.001) copy numbers of total bacteria, Lactobacillus, yeasts, and fungi than the control. The addition of PEG decreased (P < 0.01) bacterial diversity during both ensiling and aerobic exposure, whereas it increased (P < 0.05) fungal diversity during aerobic exposure. The addition of PEG at ensiling increased (P < 0.05) the abundances of Lactobacillus and Pediococcus species but decreased (P < 0.01) the abundances of Lactococcus and Leuconostoc species. Filamentous fungi were found in the microbiome at ensiling and after aerobic exposure, whereas Bacillus spp. were the dominate bacteria after aerobic exposure. In conclusion, CT decreased protein degradation and improved the aerobic stability of silage. These desirable outcomes likely reflect the ability of PPC CT to inhibit those microorganisms involved in lowering silage quality and in the production of mycotoxins.IMPORTANCE The present study reports the effects of condensed tannins on the complex microbial communities involved in ensiling and aerobic exposure of purple prairie clover. This study documents the ability of condensed tannins to lower mycotoxin production and the associated microbiome. Taxonomic bacterial community profiles were dominated by Lactobacillales after fermentation, with a notable increase in Bacillus spp. as a result of aerobic exposure. It is interesting to observe that condensed tannins decreased bacterial diversity during both ensiling and aerobic exposure but increased fungal diversity during aerobic exposure only. The present study indicates that the effects of condensed tannins on microbial communities lead to reduced lactic acid and total volatile fatty acid production, proteolysis, and mycotoxin concentration in the terminal silage and improved aerobic stability. Condensed tannins could be used as an additive to control unfavorable microbial development and maybe enhanced feed safety.

Long photoperiod affects the maize transition from vegetative to reproductive stages: a proteomic comparison between photoperiod-sensitive inbred line and its recurrent parent.

Maize (Zea mays L.) is a typical short-day plant that is produced as an important food product and industrial material. The photoperiod is one of the most important evolutionary mechanisms enabling the adaptation of plant developmental phases to changes in climate conditions. There are differences in the photoperiod sensitivity of maize inbred lines from tropical to temperate regions. In this study, to identify the maize proteins responsive to a long photoperiod (LP), the photoperiod-insensitive inbred line HZ4 and its near-isogenic line H496, which is sensitive to LP conditions, were analyzed under long-day conditions using isobaric tags for relative and absolute quantitation. We identified 5259 proteins in maize leaves exposed to the LP condition between the vegetative and reproductive stages. These proteins included 579 and 576 differentially accumulated proteins in H496 and HZ4 leaves, respectively. The differentially accumulated proteins (e.g., membrane, defense, and energy- and ribosome-related proteins) exhibited the opposite trends in HZ4 and H496 plants during the transition from the vegetative stage to the reproductive stage. These results suggest that the photoperiod-associated fragment in H496 plants considerably influences various proteins to respond to the photoperiod sensitivity. Overall, our data provide new insights into the effects of long-day treatments on the maize proteome, and may be useful for the development of new germplasm.

Characterization of Condensed Tannins from Purple Prairie Clover (Dalea purpurea Vent.) Conserved as either Freeze-Dried Forage, Sun-Cured Hay or Silage.

Conservation methods have been shown to affect forage nutrient composition and value, but little information is available about the effect of forage conservation on plant condensed tannins (CT). The objective of this study was to assess the effects of conservation method on the concentration, chemical composition and biological activity of CT. Whole-plant purple prairie clover (PPC, Dalea purpurea Vent.) was harvested at full flower and conserved as freeze-dried forage (FD), hay (HAY) or silage (SIL). Concentration of CT in conserved PPC was determined by the butanol-HCl-acetone method. Structural composition, protein-precipitation capacity and anti-bacterial activity of CT isolated from conserved forage were determined by in situ thiolytic degradation followed by HPLC-MS analysis, a protein precipitation assay using bovine serum albumin and ribulose 1,5-disphosphate carboxylase as model proteins and by an Escherichia coli (E. coli) growth test, respectively. Conservation method had no effect on concentration of total CT, but ensiling decreased (p < 0.001) extractable CT and increased (p < 0.001) protein- and fiber-bound CT. In contrast, hay-making only increased (p < 0.01) protein-bound CT. Regardless of conservation method, epigallocatechin (EGC), catechin (C) and epicatechin (EC) were the major flavan-3-ol units, and gallocatechin (GC) was absent from both terminal and extension units of PPC CT. The SIL CT had the lowest (p < 0.001) EGC, but the highest (p < 0.01) EC in the extension units. Similarly, SIL CT exhibited a lower (p < 0.001) mean degree of polymerization (mDP), but higher (p < 0.001) procyanidins (PC) than FD or HAY CT. The protein-precipitating capacity of CT in conserved PPC ranked (p < 0.001) as FD > HAY > SIL. E. coli growth n M9 medium was inhibited by 25-100 µg/mL of CT isolated from FD, HAY and SIL (p < 0.05), but preservation method had no effect on the ability of CT to inhibit bacterial growth. The results demonstrated that ensiling decreased the extractability and protein-precipitating capacity of CT by increasing the proportions of PC. Purple prairie clover conserved as hay retained more biologically active CT than if it was conserved as silage.

Effects of Octacosanol Extracted from Rice Bran on the Laying Performance, Egg Quality and Blood Metabolites of Laying Hens.

A 42-d study with 384 Hy-line brown laying hens was conducted to assess the effects of dietary octacosanol supplementation on laying performance, egg quality and blood metabolites of laying hens. Hens were randomly allocated into 4 dietary groups of 8 cages each, which were fed basal diet supplemented with 0 (Control), 9 (OCT9), 18 (OCT18), and 27 (OCT27) mg/kg diet of octacosanol isolated from rice bran, respectively. The experiment was conducted in an environmental controlled house and hens were fed twice daily for ad libitum intake. Laying performance was determined over the 42-d period, and egg quality as well as blood metabolites were estimated on d 21 and d 42. Diets in OCT18 and OCT27 increased (p<0.05) laying rate, egg weight, egg mass, egg albumen height, Haugh unit and eggshell strength on d 42, but decreased (p<0.05) feed conversion rate and levels of total cholesterol, triglyceride and low density lipoprotein cholesterol in the serum as compared to those of Control. Feed intake, yolk color, yolk diameter, eggshell thickness and high density lipoprotein cholesterol were similar (p>0.05) among treatments. Results demonstrate that supplementing 18 to 27 mg/kg diet of rice bran octacosanol can improve laying rate and egg quality and reduce blood lipid of laying hens.

Phosphoproteomic analysis of the resistant and susceptible genotypes of maize infected with sugarcane mosaic virus.

Protein phosphorylation plays a pivotal role in the regulation of many cellular events. No information is yet available, however, on protein phosphorylation in plants in response to virus infection. In this study, we characterized phosphoproteomes of resistant and susceptible genotypes of maize (Zea mays L.) in response to Sugarcane mosaic virus (SCMV) infection. Based on isotope tags for relative and absolute quantification technology, TiO2 enrichment method and LC-MS/MS analysis, we identified 65 and 59 phosphoproteins respectively, whose phosphorylation level regulated significantly in susceptible and resistant plants. Some identified phosphoproteins were shared by both genotypes, suggesting a partial overlapping of the responsive pathways to virus infection. While several phosphoproteins are well-known pathogen response phosphoproteins, virus infection differentially regulates most other phosphoproteins, which has not been reported in literature. Changes in protein phosphorylation status indicated that response to SCMV infection encompass a reformatting of major cellular processes. Our data provide new valuable insights into plant-virus interactions.

Readthrough events in plants reveal plasticity of stop codons.

Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor tRNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of basic transcription factor 3. Furthermore, the SCR events exhibit non-conserved signature, and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.

Ovary Abortion Induced by Combined Waterlogging and Shading Stress at the Flowering Stage Involves Amino Acids and Flavonoid Metabolism in Maize.

Maize (Zea mays L.) crops on the North China Plain are often subject to continuous overcast rain at the flowering stage. This causes waterlogging and shading stresses simultaneously and leads to huge yield losses, but the causes of these yield losses remain largely unknown. To explore the factors contributing to yield loss caused by combined waterlogging and shading stress at the flowering stage, we performed phenotypic, physiological, and quasi-targeted metabolomics analyses of maize plants subjected to waterlogging, shading, and combined waterlogging and shading (WS) treatments. Analyses of phenotypic and physiological indexes showed that, compared with waterlogging or shading alone, WS resulted in lower source strength, more severe inhibition of ovary and silk growth at the ear tip, a reduced number of emerged silks, and a higher rate of ovary abortion. Changes in carbon content and enzyme activity could not explain the ovary abortion in our study. Metabolomic analyses showed that the events occurred in ovaries and silks were closely related to abortion, WS forced the ovary to allocate more resources to the synthesis of amino acids involved in the stress response, inhibited the energy metabolism, glutathione metabolism and methionine salvage pathway, and overaccumulation of H2O2. In silks, WS led to lower accumulation levels of specific flavonoid metabolites with antioxidant capacity, and to over accumulation of H2O2. Thus, compared with each single stress, WS more seriously disrupted the normal metabolic process, and resulted more serious oxidative stress in ovaries and silks. Amino acids involved in the stress response in ovaries and specific flavonoid metabolites with antioxidant capacity in silks play important roles during ovary abortion. These results identify novel traits for selection in breeding programs and targets for genome editing to increase maize yield under WS stress.

Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline.

Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. In this study, we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. These NCPs showed distinct characteristics compared with conventional peptides and were derived from introns, 3' UTRs, 5' UTRs, junctions, and intergenic regions. Furthermore, our results showed that translation events in unannotated transcripts occur more broadly than previously thought. In addition, we found that dozens of maize NCPs are enriched within regions associated with phenotypic variations and domestication selection, indicating that they potentially are involved in genetic regulation of complex traits and domestication in maize. Taken together, our study developed an integrated peptidogenomic pipeline for large-scale identification of NCPs in plants, which would facilitate global characterization of NCPs from other plants. The identification of large-scale NCPs in both monocot (maize) and dicot (Arabidopsis) plants indicates that a large portion of plant genome can be translated into biologically functional molecules, which has important implications for functional genomic studies.

Alternative splicing of ZmCCA1 mediates drought response in tropical maize.

The circadian clock regulates numerous biological processes in plants, especially development and stress responses. CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) is one of the core components of the day-night rhythm response and is reportedly associated with ambient temperature in Arabidopsis thaliana. However, it remains unknown if alternative splicing of ZmCCA1 is modulated by external stress in maize, such as drought stress and photoperiod. Here, we identified three ZmCCA1 splice variants in the tropical maize line CML288, which are predicted to encode three different protein isoforms, i.e., ZmCCA1.1, ZmCCA1.2, and ZmCCA1.3, which all retain the MYB domain. In maize, the expression levels of ZmCCA1 splice variants were influenced by photoperiod, tissue type, and drought stress. In transgenic A. thaliana, ZmCCA1.1 may be more effective than ZmCCA1.3 in increasing drought tolerance while ZmCCA1.2 may have only a small effect on tolerance to drought stress. Additionally, although CCA1 genes have been found in many plant species, alternative CCA1 splicing events are known to occur in species-specific ways. Our study provides new sight to explore the function of ZmCCA1 splice variants' response to abiotic stress, and clarify the linkage between circadian clock and environmental stress in maize.

Comparative proteomic analysis of the maize responses to early leaf senescence induced by preventing pollination.

The aim of this study was to explore the molecular mechanisms of induced leaf senescence by preventing pollination in maize using a proteomic method combined with other physiological methods. An elite maize inbred line Yu816 was selected for evaluation of its senescence mechanism. Phenotypic and chlorophyll content analysis revealed that the onset of leaf senescence occurred earlier in non-pollinated (NONPOL) leaves than pollinated (POL) leaves. Leaf protein species of NONPOL and POL leaves were separately extracted and their proteomes were assessed using isobaric tags for relative and absolute quantitation (iTRAQ) analysis. A total of 4371 protein species were identified, of which 809 exhibited differentially altered abundance (P < 0.05). The identified protein species were related to diverse functions including photosystems, plant hormones, cell death, oxidative degradation, and protein metabolism, suggesting a potential signaling cascade for ear leaf senescence induced by pollination prevention. In addition, leaf total soluble sugar and leaf starch contents were remarkably higher in NONPOL plants than in POL plants. These findings suggest that induced leaf senescence might be associated with nutrient remobilization. Our results reveal a network of molecular mechanisms at the protein level and provide some insights into the early senescence mechanism in higher plants. Biological significance: The coordination between growth and timing for senescence is critical for maize production. However, the molecular mechanism of induced leaf senescence by preventing pollination in maize remains to be further elucidated at the proteomic level. Herein, we revealed some new protein species that are involved in hormone signaling, glycometabolism, oxidation-reduction, protein degradation and photosystem breakdown, and other biological processes that were not previously known to be associated with leaf senescence. This is the first large-scale proteomics study to examine induced leaf senescence in maize by preventing pollination.

Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination-prevention.

In maize (Zea mays), leaf senescence acts as a nutrient recycling process involved in proteins, lipids, and nucleic acids degradation and transport to the developing sink. However, the molecular mechanisms of pre-maturation associated with pollination-prevention remain unclear in maize. To explore global gene expression changes during the onset and progression of senescence in maize, the inbred line 08LF, with severe early senescence caused by pollination prevention, was selected. Phenotypic observation showed that the onset of leaf senescence of 08LF plants occurred approximately 14 days after silking (DAS) by pollination prevention. Transcriptional profiling analysis of the leaf at six developmental stages during induced senescence revealed that a total of 5,432 differentially expressed genes (DEGs) were identified, including 2314 up-regulated genes and 1925 down-regulated genes. Functional annotation showed that the up-regulated genes were mainly enriched in multi-organism process and nitrogen compound transport, whereas down-regulated genes were involved in photosynthesis. Expression patterns and pathway enrichment analyses of early-senescence related genes indicated that these DEGs are involved in complex regulatory networks, especially in the jasmonic acid pathway. In addition, transcription factors from several families were detected, particularly the CO-like, NAC, ERF, GRAS, WRKY and ZF-HD families, suggesting that these transcription factors might play important roles in driving leaf senescence in maize as a result of pollination-prevention.