Differential effects of winter cold stress on soil bacterial communities, metabolites, and physicochemical properties in two varieties of Tetrastigma hemsleyanum Diels & Gilg in reclaimed land.

Tetrastigma hemsleyanum Diels & Gilg (TDG) has been recently planted in reclaimed lands in Zhejiang Province, China, to increase reclaimed land use. Winter cold stress seriously limits the growth and development of TDG and has become the bottleneck limiting the TDG planting industry. To investigate the defense mechanisms of TDG toward winter cold stress when grown on reclaimed land, a combined analysis of soil bacterial communities, metabolites, and physicochemical properties was conducted in this study. Significant differences were observed in the composition of soil bacterial communities, metabolites, and properties in soils of a cold-tolerant variety (A201201) compared with a cold-intolerant variety (B201810). The fresh weight (75.8% of tubers) and dry weight (73.6%) of A201201 were significantly higher than those of B201810. The 16S rRNA gene amplicon sequencing of soil bacteria showed that Gp5 (25.3%), Gemmatimonas (19.6%), Subdivision3 (16.7%), Lacibacterium (11.9%), Gp4 (11.8%), Gp3 (10.4%), Gp6 (7.0%), and WPS-1 (1.2%) were less common, while Chryseolinea (10.6%) were more common in A201201 soils than B201810 soils. Furthermore, linear discriminant analysis of effect size identified 35 bacterial biomarker taxa for both treatments. Co-occurrence network analyses also showed that the structures of the bacterial communities were more complex and stable in A201201 soils compared to B201810 soils. In addition, ultra-high-performance liquid chromatography coupled to mass spectrometry analysis indicated the presence of significantly different metabolites in the two soil treatments, with 10 differentially expressed metabolites (DEMs) (8 significantly upregulated by 9.2%-391.3% and 2 significantly downregulated by 25.1%-73.4%) that belonged to lipids and lipid-like molecules, organic acids and derivatives, and benzenoids. The levels of those DEMs were significantly correlated with the relative abundances of nine bacterial genera. Also, redundancy discriminant analysis revealed that the main factors affecting changes in the bacterial community composition were available potassium (AK), microbial biomass nitrogen (MBN), microbial biomass carbon (MBC), alkaline hydrolysis nitrogen (AHN), total nitrogen (TN), available phosphorus (AP), and soil organic matter (SOM). The main factors affecting changes in the metabolite profiles were AK, MBC, MBN, AHN, pH, SOM, TN, and AP. Overall, this study provides new insights into the TDG defense mechanisms involved in winter cold stress responses when grown on reclaimed land and practical guidelines for achieving optimal TDG production.IMPORTANCEChina has been undergoing rapid urbanization, and land reclamation is regarded as a viable option to balance occupation and compensation. In general, the quality of reclaimed land cannot meet plant or even cultivation requirements due to poor soil fertility and high gravel content. However, Tetrastigma hemsleyanum Diels & Gilg (TDG), extensively used in Chinese herbal medicine, can grow well in stony soils with few nutrients. So, to increase reclaimed land use, TDG has been cultivated on reclaimed lands in Zhejiang Province, China, recently. However, the artificial cultivation of TDG is often limited by winter cold stress. The aim of this study was to find out how TDG on reclaimed land deal with winter cold stress by looking at the bacterial communities, metabolites, and physicochemical properties of the soil, thereby guiding production in practice.

Exogenous titanium dioxide nanoparticles alleviate cadmium toxicity by enhancing the antioxidative capacity of Tetrastigma hemsleyanum.

Nanotechnology is one of the most recent approaches employed to defend plants against both biotic and abiotic stress including heavy metals such as Cadmium (Cd). In this study, we evaluated the effects of titanium dioxide (TiO2) nanoparticles (TiO2 NPs) in alleviating Cd stress in Tetrastigma hemsleyanum Diels et Gilg. Compared with Cd treatment, TiO2 NPs decreased leaf Cd concentration, restored Cd exposure-related reduction in the biomass to about 69% of control and decreased activities of antioxidative enzymes. Integrative analysis of transcriptome and metabolome revealed 325 differentially expressed genes associated with TiO2 NP treatment, most of which were enriched in biosynthesis of secondary metabolites. Among them, the flavonoid and phenylpropanoid biosynthetic pathways were significantly regulated to improve the growth of T. hemsleyanum when treated with Cd. In the KEGG Markup Language (KGML) network analysis, we found some commonly regulated pathways between Cd and Cd+TiO2 NP treatment, including phenylpropanoid biosynthesis, ABC transporters, and isoflavonoid biosynthesis, indicating their potential core network positions in controlling T. hemsleyanum response to Cd stress. Overall, our findings revealed a complex response system for tolerating Cd, encompassing the transportation, reactive oxygen species scavenging, regulation of gene expression, and metabolite accumulation in T. hemsleyanum. Our results indicate that TiO2 NP can be used to reduce Cd toxicity in T. hemsleyanum.

Cadmium induced a non-coding RNA microRNA535 mediates Cd accumulation in rice.

Identifying key regulators related to cadmium (Cd) tolerance and accumulation is the main factor for genetic engineering to improve plants for bioremediation and ensure crop food safety. MicroRNAs (miRNAs), as fine-tuning regulators of genes, participate in various abiotic stress processes. MiR535 is an ancient conserved non-coding small RNA in land plants, positively responding to Cd stress. We investigated the effects of knocking out (mir535) and overexpressing miR535 (mir535 and OE535) under Cd stress in rice plants in this study. The mir535 plants showed better Cd tolerance than wild type (WT), whereas the OE535 showed the opposite effect. Cd accumulated approximately 71.9% and 127% in the roots of mir535 and OE535 plants, respectively, compared to WT, after exposure to 2 µmol/L Cd. In brown rice, the total Cd accumulation of OE535 and mir535 was about 78% greater and 35% lower than WT. When growing in 2 mg/kg Cd of soil, the Cd concentration was significantly lower in mir535 and higher in OE535 than in the WT; afterward, we further revealed the most possible target gene SQUAMOSA promoter binding-like transcription factor 7(SPL7) and it negatively regulates Nramp5 expression, which in turn regulates Cd metabolism. Therefore, the CRISPR/Cas9 technology may be a valuable strategy for creating new rice varieties to ensure food safety.

Role of plant metabolites in the formation of bacterial communities in the rhizosphere of Tetrastigma hemsleyanum.

Tetrastigma hemsleyanum Diels et Gilg, commonly known as Sanyeqing (SYQ), is an important traditional Chinese medicine. The content of bioactive constituents varies in different cultivars of SYQ. In the plant growth related researches, rhizosphere microbiome has gained significant attention. However, the role of bacterial communities in the accumulation of metabolites in plants have not been investigated. Herein, the composition of bacterial communities in the rhizosphere soils and the metabolites profile of different SYQ cultivars' roots were analyzed. It was found that the composition of microbial communities varied in the rhizosphere soils of different SYQ cultivars. The high abundance of Actinomadura, Streptomyces and other bacteria was found to be associated with the metabolites profile of SYQ roots. The findings suggest that the upregulation of rutin and hesperetin may contribute to the high bioactive constituent in SYQ roots. These results provide better understanding of the metabolite accumulation pattern in SYQ, and also provide a solution for enhancing the quality of SYQ by application of suitable microbial consortia.

Comparative Analysis of Proanthocyanidin Metabolism and Genes Regulatory Network in Fresh Leaves of Two Different Ecotypes of Tetrastigma hemsleyanum.

Tetrastigma hemsleyanum Diels et Gilg is a rare and wild medicinal resource. Metabolites, especially secondary metabolites, have an important influence on T. hemsleyanum adaptability and its medicinal quality. The metabolite proanthocyanidin (PA) is a polyphenol compound widely distributed in land plants, which can be used as antioxidants and anticancer agents. Here, we discovered that three types of PA accumulated in large amounts in purple leaves (PL), but not in green leaves (RG), based on widely non-targeted metabolomics. In addition, we further found that catechins and their derivatives, which are the structural units of PA, are also enriched in PL. Afterwards, we screened and obtained five key genes, DNR1/2, ANS, ANR and LAR closely related to PA biosynthesis through transcriptome analysis and found they were all highly expressed in PL compared to RG. Therefore, observed the regulatory relationship between the main compounds and genes network, and the PA metabolism regulatory pathway was complicated, which may be different to other species.

Transcriptome and Metabolome Integrated Analysis of Two Ecotypes of Tetrastigma hemsleyanum Reveals Candidate Genes Involved in Chlorogenic Acid Accumulation.

T. hemsleyanum plants with different geographical origins contain enormous genetic variability, which causes different composition and content of flavonoids. In this research, integrated analysis of transcriptome and metabolome were performed in two ecotypes of T. hemsleyanum. There were 5428 different expressed transcripts and 236 differentially accumulated metabolites, phenylpropane and flavonoid biosynthesis were most predominantly enriched. A regulatory network of 9 transcripts and 11 compounds up-regulated in RG was formed, and chlorogenic acid was a core component.

Transcriptome-Based Analysis of Phosphite-Induced Resistance Against Pathogens in Rice.

Phosphite (PHI) has been used in the management of Phytophthora diseases since the 1970s.We assessed the effect of PHI on controlling the incidence of Xanthomonas oryzae pv.oryzae and Pyricularia grisea. As a result, PHI application significantly inhibited the incidence of the diseases. To clarify the molecular mechanism underlying this, a transcriptome study was employed. In total, 2064 differentially expressed genes (DEGs) were identified between control and PHI treatment. The key DEGs could be classified into phenylpropanoid biosynthesis (ko00940), starch and sucrose metabolism (ko00500), and plant hormone signal transduction (ko04075). The expressions of defense-related genes had a higher expression lever upon PHI treatment. This study provides new insights into the mechanism of protection effect of PHI against pathogens.

Nystose regulates the response of rice roots to cold stress via multiple signaling pathways: A comparative proteomics analysis.

Small fructans improve plant tolerance for cold stress. However, the underlying molecular mechanisms are poorly understood. Here, we have demonstrated that the small fructan tetrasaccharide nystose improves the cold stress tolerance of primary rice roots. Roots developed from seeds soaked in nystose showed lower browning rate, higher root activity, and faster growth compared to seeds soaked in water under chilling stress. Comparative proteomics analysis of nystose-treated and control roots identified a total of 497 differentially expressed proteins. GO classification and KEGG pathway analysis documented that some of the upregulated differentially expressed proteins were implicated in the regulation of serine/threonine protein phosphatase activity, abscisic acid-activated signaling, removal of superoxide radicals, and the response to oxidative stress and defense responses. Western blot analysis indicated that nystose promotes the growth of primary rice roots by increasing the level of RSOsPR10, and the cold stress-induced change in RSOsPR10levelis regulated by jasmonate, salicylic acid, and abscisic acid signaling pathways in rice roots. Furthermore, OsMKK4-dependentmitogen-activated protein kinase signaling cascades may be involved in the nystose-induced cold tolerance of primary rice roots. Together, these results indicate that nystose acts as an immunostimulator of the response to cold stress by multiple signaling pathways.

Oxidative stress response mechanism of Scenedesmus obliquus to ionic liquids with different number of methyl-substituents.

Ionic liquids (ILs) have become persistent contaminants in water because of their good solubility and low biodegradability. The oxidative stress responses of Scenedesmus obliquus to three imidazole ILs with different number of methyl-substituents, i.e., 1-decyl-imidazolium chloride ([C10IM]Cl), 1-decyl-3-methylimidazolium chloride ([C10MIM]Cl), and 1-decyl-2,3-dimethylimidazolium chloride ([C10DMIM]Cl), were studied. There was a positive correlation between ROS level and IL concentration. The activities of antioxidant enzymes, i.e., superoxide dismutase, catalase, peroxidase, ascorbate peroxidase, and glutathione peroxidase, and the content of antioxidants, i.e., ascorbic acid and glutathione, changed in IL treatment with a concentration-dependent effect. Proline accumulation increased with increasing IL concentration. Integrated biomarker response (IBR) index analysis, based on the eight oxidative stress response indicators, revealed that the toxicity order was: [C10IM]Cl < [C10DMIM]Cl < [C10MIM]Cl. Proteomic analysis showed that IL affect the type and distribution of proteins in S. obliquus. Chloroplast and photosystem II were affected as cellular component, and the proteins related to oxidative stress are annotated in GO categories. IBR index and proteomic analysis indicate that oxidative stress response is one of the main biomarkers of IL stress.

Integrated analysis of the transcriptome and metabolome of purple and green leaves of Tetrastigma hemsleyanum reveals gene expression patterns involved in anthocyanin biosynthesis.

To gain better insight into the regulatory networks of anthocyanin biosynthesis, an integrated analysis of the metabolome and transcriptome in purple and green leaves of Tetrastigma hemsleyanum was conducted. Transcript and metabolite profiles were archived by RNA-sequencing data analysis and LC-ESI-MS/MS, respectively. There were 209 metabolites and 4211 transcripts that were differentially expressed between purple and green leaves. Correlation tests of anthocyanin contents and transcriptional changes showed 141 significant correlations (Pearson correlation coefficient >0.8) between 16 compounds and 14 transcripts involved in the anthocyanin biosynthesis pathway. Some novel genes and metabolites were discovered as potential candidate targets for the improvement of anthocyanin content and superior cultivars.

Oxidative stress response and proteomic analysis reveal the mechanisms of toxicity of imidazolium-based ionic liquids against Arabidopsis thaliana.

Ionic liquids (ILs) are extensively used in various fields, posing a potential threat in the ecosystem because of their high stability, excellent solubility, and biological toxicity. In this study, the toxicity mechanism of three ILs, 1-octyl-3-methylimidazolium chloride ([C8MIM]Cl), 1-decyl-3-methylimidazolium chloride ([C10MIM]Cl), and 1-dodecyl-3-methylimidazolium chloride ([C12MIM]Cl) on Arabidopsis thaliana were revealed. Reactive oxygen species (ROS) level increased with higher concentration and longer carbon chain length of ILs, which led to the increase of malondialdehyde (MDA) content and antioxidase activity, including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX) and peroxidase (POD) activities. SOD, CAT, and GPX activities decreased in high ILs concentration due to the excessive ROS. Differentially expressed protein was analyzed based on Gene ontology (GO) and KEGG pathways analysis. 70, 45, 84 up-regulated proteins, and 72, 104, 79 down-regulated proteins were identified in [C8MIM]Cl, [C10MIM]Cl, and [C12MIM]Cl treatment, respectively (fold change ≥ 1.5 with ≥95% confidence). Cellular aldehyde metabolic process, mitochondrial and mitochondrial respiratory chains, glutathione transferase and oxidoreductase activity were enriched as up-regulated proteins as the defense mechanism of A. thaliana to resist external stresses. Chloroplast, photosynthetic membrane and thylakoid, structural constituent of ribosome, and transmembrane transport were enriched as the down-regulated protein. Compared with the control, 8 and 14 KEGG pathways were identified forup-regulated and down-regulated proteins, respectively, in three IL treatments. Metabolic pathways, carbon metabolism, biosynthesis of amino acids, porphyrin and chlorophyll metabolism were significantly down-regulated. The GO terms annotation demonstrated the oxidative stress response and effects on photosynthesis of A. thaliana in ILs treatment from biological process, cellular component, and molecular function categories.

Proteomic analysis of 2-chloroethanol extracts of rice (Oryza sativa L.) seeds.

Ethanol-soluble proteins, including prolamins, are one of the most important seed proteins in rice (Oryza sativa L.). However, little is known about the proteomic profile of ethanol-soluble protein fraction extracted from rice grain. In this work, the differential profile of ethanol-soluble proteins extracted by 2-chloroethanol and ethanol has been documented. Proteome analysis utilizing LC-MS/MS identified a total of 64 unique proteins in the 2-chloroethanol extract of rice seeds. The majority of these proteins had low molecular weight ranging from 10 to 25 kD and isoelectric point (pI) in mid-acidic (pH 5-pH 7) and mid-basic (pH 7-pH 9) ranges. Database searches combined with transmembrane domain (TMD) analysis revealed that >70% of identified proteins were hydrophobic, i.e., had at least one TMD. Gene ontology classification and enrichment analysis showed that the identified proteins were involved in13 types of biological processes, 5 types of cell components, and 17 types of molecular functions. These results were significant based on the hyper p-value of <0.05. The most frequent categories of biological processes, cell components, and molecular functions were, respectively, type I hypersensitivity, extracellular space and extracellular region, and serine-type endopeptidase inhibitor activity. Interestingly, in addition to seed storage proteins such as prolamins and glutelins, certain allergen proteins, protease inhibitors, and lipid transfer proteins were identified in the extracts. Together, the collected data provide novel insights into the protein profile of 2-chloroethanol extract of rice seeds.

Comparative Transcriptome Analysis Reveals the Transcriptional Alterations in Growth- and Development-Related Genes in Sweet Potato Plants Infected and Non-Infected by SPFMV, SPV2, and SPVG.

Field co-infection of multiple viruses results in considerable losses in the yield and quality of storage roots in sweet potato. However, little is known about the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses. Here, a comparative transcriptomic analysis was performed to reveal the transcriptional alterations in sweet potato plants infected (VCSP) and non-infected (VFSP) by Sweet potato mild mottle virus (SPFMV), Sweet potato virus Y (SPV2) and Sweet potato virus G (SPVG). A total of 1580 and 12,566 differentially expressed genes (DEGs) were identified in leaves and storage roots of VFSP and VCSP plants, respectively. In leaves, 707 upregulated and 773 downregulated genes were identified, whereas 5653 upregulated and 6913 downregulated genes were identified in storage roots. Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in chloroplast and photosynthesis and brassinosteroid (BR) biosynthesis in leaves and the vitamin biosynthetic process in storage roots was inhibited by co-infection of three viruses: SPFMV, SPV2, and SPVG. This was likely closely related to better photosynthesis and higher contents of Vitamin C (Vc) in storage roots of VFSP than that of VCSP. While some genes involved in ribosome and secondary metabolite-related pathways in leaves and alanine, aspartate, and glutamate metabolism in storage roots displayed higher expression in VCSP than in VFSP. Quantitative real-time PCR analysis demonstrated that the expression patterns of 26 DEGs, including 16 upregulated genes and 10 downregulated genes were consistent with the RNA-seq data from VFSP and VCSP. Taken together, this study integrates the results of morphology, physiology, and comparative transcriptome analyses in leaves and storage roots of VCSP and VFSP to reveal transcriptional alterations in growth- and development-related genes, providing new insight into the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses.

A zinc finger protein, interacted with cyclophilin, affects root development via IAA pathway in rice.

The plant hormone auxin plays a crucial role in lateral root development. To better understand the molecular mechanisms underlying lateral root formation, an auxin-responsive gene OsCYP2 (Os02g0121300) was characterized from rice. Compared to the wild type, OsCYP2-RNAi (RNA interference) lines exhibited distinctive defects in lateral root development. Yeast two-hybrid and glutathione S-transferase pull-down results confirmed that OsCYP2 interacted with a C2HC-type zinc finger protein (OsZFP, Os01g0252900) which is located in the rice nucleus. T2 OsZFP-RNAi lines had significantly fewer lateral roots than did wild-type plants, which suggests a role for OsCYP2 and OsZFP in regulating lateral root development. Quantitative real-time polymerase chain reaction showed that the expression of certain Aux/IAA (auxin/indole-3-acetic acid) genes was altered in OsCYP2- and OsZFP-RNAi lines in response to IAA. These findings imply that OsCYP2 and OsZFP participate in IAA signal pathways controlling lateral root development. More importantly, OsIAA11 showed functional redundancy not only in OsCYP2-RNAi lines but also in OsZFP-RNAi lines, which provides important clues for the elucidation of mechanisms controlling lateral root development in response to auxin.

Comparative transcriptome analysis reveals the transcriptional alterations in heat-resistant and heat-sensitive sweet maize (Zea mays L.) varieties under heat stress.

BACKGROUND: Despite the heat-related physiology and heat-shock proteins in maize have been extensively studied, little is known about the transcriptome profiling of how the maize varieties with different genotypes responding to high temperatures. Seedling mortality of Xiantian 5 (XT) is significantly lower than that of Zhefengtian (ZF) when exposed to high temperature (42 °C for 6 h) and followed by a recovery growth (25 °C for one week). Therefore, we performed a transcriptome analysis using the total RNA extracted from the leaves of XT and ZF that were previously subjected to heat stress at 42 °C for 0 h, 0.5 h, and 3 h, respectively. RESULTS: A total of 516 commonly up-regulated and 1,261 commonly down-regulated genes were identified among XT/ZF, XT0.5/ZF0.5 and XT3/ZF3 using transcriptome analysis. Gene Ontology classification of the 516 up-regulated genes showed that their encoded proteins were significantly assigned to 18 cellular components, and were classified into 9 functional categories, and were involved in 9 biological processes. Most of proteins encoded by up-regulated genes were localized in chloroplast and its structural components, and involved in multiple biological processes associated with photosynthesis, indicating that these chloroplast proteins play an important role in increasing heat tolerance in sweet maize. While the proteins encoded by 1,261 down-regulated genes were significantly assigned to 31 cellular components, and were classified into 3 functional categories, and were involved in 9 biological processes. Interestingly, these proteins were involved in a series of biological processes from gene expression to translation, suggesting that lowering these processes may contribute to improved heat resistance in sweet maize. The up-regulated genes were identified to be involved in 36 distinct metabolic pathways, of which the most significant ones was secondary metabolite biosynthetic pathway. While the down-regulated genes were identified to be involved in 23 distinct metabolic pathways, of which the most significant ones were found in ribosome. Quantitative real-time PCR analysis demonstrated that 5 genes involved in the biosynthesis of secondary metabolites and photosynthesis in XT have higher abundance than those in ZF, whereas 5 ribosome genes in XT showed lower abundance than those in ZF. In addition, heat-tolerant sweet maize may keep at lower growth level than heat-sensitive one through dowregulating expression of genes related to zeatin and brassinosteroid biosynthesis to better regulate heat stress responses. CONCLUSIONS: Comparative transcriptomic profiling reveals transcriptional alterations in heat-resistant and heat-sensitive sweet maize varieties under heat stress, which provides a new insight into underlying molecular mechanism of maize in response to heat stress.

OsPEX11, a Peroxisomal Biogenesis Factor 11, Contributes to Salt Stress Tolerance in Oryza sativa.

Peroxisomes are single membrane-bound organelles, whose basic enzymatic constituents are catalase and H2O2-producing flavin oxidases. Previous reports showed that peroxisome is involved in numerous processes including primary and secondary metabolism, plant development and abiotic stress responses. However, knowledge on the function of different peroxisome genes from rice and its regulatory roles in salt and other abiotic stresses is limited. Here, a novel prey protein, OsPEX11 (Os03g0302000), was screened and identified by yeast two-hybrid and GST pull-down assays. Phenotypic analysis of OsPEX11 overexpression seedlings demonstrated that they had better tolerance to salt stress than wild type (WT) and OsPEX11-RNAi seedlings. Compared with WT and OsPEX11-RNAi seedlings, overexpression of OsPEX11 had lower level of lipid peroxidation, Na+/K+ ratio, higher activities of antioxidant enzymes (SOD, POD, and CAT) and proline accumulation. Furthermore, qPCR data suggested that OsPEX11 acted as a positive regulator of salt tolerance by reinforcing the expression of several well-known rice transporters (OsHKT2;1, OsHKT1;5, OsLti6a, OsLti6b, OsSOS1, OsNHX1, and OsAKT1) involved in Na+/K+ homeostasis in transgenic plants under salinity. Ultrastructural observations of OsPEX11-RNAi seedlings showed that they were less sensitive to salt stress than WT and overexpression lines. These results provide experimental evidence that OsPEX11 is an important gene implicated in Na+ and K+ regulation, and plays a critical role in salt stress tolerance by modulating the expression of cation transporters and antioxidant defense. Thus, OsPEX11 could be considered in transgenic breeding for improvement of salt stress tolerance in rice crop.

Comparative proteomic analysis reveals alterations in development and photosynthesis-related proteins in diploid and triploid rice.

BACKGROUND: Polyploidy has pivotal influences on rice (Oryza sativa L.) morphology and physiology, and is very important for understanding rice domestication and improving agricultural traits. Diploid (DP) and triploid (TP) rice shows differences in morphological parameters, such as plant height, leaf length, leaf width and the physiological index of chlorophyll content. However, the underlying mechanisms determining these morphological differences are remain to be defined. To better understand the proteomic changes between DP and TP, tandem mass tags (TMT) mass spectrometry (MS)/MS was used to detect the significant changes to protein expression between DP and TP. RESULTS: Results indicated that both photosynthesis and metabolic pathways were highly significantly associated with proteomic alteration between DP and TP based on biological process and pathway enrichment analysis, and 13 higher abundance chloroplast proteins involving in these two pathways were identified in TP. Quantitative real-time PCR analysis demonstrated that 5 of the 13 chloroplast proteins ATPF, PSAA, PSAB, PSBB and RBL in TP were higher abundance compared with those in DP. CONCLUSIONS: This study integrates morphology, physiology and proteomic profiling alteration of DP and TP to address their underlying different molecular mechanisms. Our finding revealed that ATPF, PSAA, PSAB, PSBB and RBL can induce considerable expression changes in TP and may affect the development and growth of rice through photosynthesis and metabolic pathways.

Effects of the Herbicide Imazethapyr on Photosynthesis in PGR5- and NDH-Deficient Arabidopsis thaliana at the Biochemical, Transcriptomic, and Proteomic Levels.

Photosynthesis is a very important metabolic pathway for plant growth and crop yield. This report investigated the effect of the herbicide imazethapyr on photosynthesis in the Arabidopsis thaliana pnsB3 mutant (a defect in the NDH pathway) and pgr5 mutant (a defect in the PGR5 pathway) to determine which cyclic electron transport chain (CET) of the NDH and PGR5 pathways is more important for protecting the photosynthetic system under herbicide stress. The results showed that 20 µg/L imazethapyr markedly inhibited the growth of the three ecotypes of A. thaliana and produced more anthocyanins and reactive oxygen species (ROS), particularly in the pgr5 mutant. The chlorophyll fluorescence results showed that PSII was severely damaged in the pgr5 mutant. Additionally, the CET was significantly stimulated to protect the photosynthetic system from light damage in Wt and the pnsB3 mutant but not the pgr5 mutant. The real-time PCR analysis indicated that imazethapyr treatment considerably decreased the transcript levels of most photosynthesis-related genes in the three treated groups. Several genes in the PGR5 pathway were significantly induced in the pnsB3 mutant, but no genes in the NDH pathway were induced in the pgr5 mutant. The gene transcription analysis showed that the pgr5 mutant cannot compensate for the deficit in the PGR5 pathway by stimulating the NDH pathway, whereas the pnsB3 mutant can compensate for the deficit in the CET cycle by regulating the PGR5 pathway. The iTRAQ analyses also showed that the photosynthesis system, glycolysis, and TCA cycle suffered the most severe damage in the pgr5 mutant. All of these results showed that the PGR5 pathway is more critical for electron transfer around PSI than the NDH pathway to resist herbicide stress.

Global analysis of lysine acetylation in strawberry leaves.

Protein lysine acetylation is a reversible and dynamic post-translational modification. It plays an important role in regulating diverse cellular processes including chromatin dynamic, metabolic pathways, and transcription in both prokaryotes and eukaryotes. Although studies of lysine acetylome in plants have been reported, the throughput was not high enough, hindering the deep understanding of lysine acetylation in plant physiology and pathology. In this study, taking advantages of anti-acetyllysine-based enrichment and high-sensitive-mass spectrometer, we applied an integrated proteomic approach to comprehensively investigate lysine acetylome in strawberry. In total, we identified 1392 acetylation sites in 684 proteins, representing the largest dataset of acetylome in plants to date. To reveal the functional impacts of lysine acetylation in strawberry, intensive bioinformatic analysis was performed. The results significantly expanded our current understanding of plant acetylome and demonstrated that lysine acetylation is involved in multiple cellular metabolism and cellular processes. More interestingly, nearly 50% of all acetylated proteins identified in this work were localized in chloroplast and the vital role of lysine acetylation in photosynthesis was also revealed. Taken together, this study not only established the most extensive lysine acetylome in plants to date, but also systematically suggests the significant and unique roles of lysine acetylation in plants.

Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.).

Rice hull, the outer cover of the rice grain, determines grain shape and size. Changes in the rice hull proteome in different growth stages may reflect the underlying mechanisms involved in grain development. To better understand these changes, isobaric tags for relative and absolute quantitative (iTRAQ) MS/MS was used to detect statistically significant changes in the rice hull proteome in the booting, flowering, and milk-ripe growth stages. Differentially expressed proteins were analyzed to predict their potential functions during development. Gene ontology (GO) terms and pathways were used to evaluate the biological mechanisms involved in rice hull at the three growth stages. In total, 5,268 proteins were detected and characterized, of which 563 were differentially expressed across the development stages. The results showed that the flowering and milk-ripe stage proteomes were more similar to each other (r=0.61) than either was to the booting stage proteome. A GO enrichment analysis of the differentially expressed proteins was used to predict their roles during rice hull development. The potential functions of 25 significantly differentially expressed proteins were used to evaluate their possible roles at various growth stages. Among these proteins, an unannotated protein (Q7X8A1) was found to be overexpressed especially in the flowering stage, while a putative uncharacterized protein (B8BF94) and an aldehyde dehydrogenase (Q9FPK6) were overexpressed only in the milk-ripe stage. Pathways regulated by differentially expressed proteins were also analyzed. Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), and two magnesium-chelatase subunits, ChlD (Q6ATS0), and ChlI (Q53RM0), were associated with chlorophyll biosynthesis at different developmental stages. The expression of Q9SDJ2 in the flowering and milk-ripe stages was validated by qRT-PCR. The 25 candidate proteins may be pivotal markers for controlling rice hull development at various growth stages and chlorophyll biosynthesis pathway related proteins, especially magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), may provide new insights into the molecular mechanisms of rice hull development and chlorophyll associated regulation.