Integration of the proteome and transcriptome reveals multiple levels of gene regulation in the rice dl2 mutant

Integration of Epigenome and Lactylome Reveals the Regulation of Lipid Production in Nannochloropsis oceanica

Lysine lactylation (Kla) is a kind of novel post-translational modification (PTM) that participates in gene expression and various metabolic processes. Nannochloropsis has a remarkable capacity for triacylglycerol (TAG) production under nitrogen stress. To elucidate the involvement of lactylation in lipid synthesis, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) and mRNA-seq analyses to monitor lactylation modifications and transcriptome alterations in Nannochloropsis oceanica. In all, 2057 genes showed considerable variation between nitrogen deprivation (ND) and nitrogen repletion (NR) conditions. Moreover, a total of 5375 differential Kla peaks were identified, including 5331 gain peaks and 44 loss peaks under ND vs NR. The differential Kla peaks were primarily distributed in the promoter (≤1 kb) (71.07%), 5'UTR (22.64%), and exon (4.25%). Integrative analysis of ChIP-seq, transcriptome, and previous proteome and lactylome data elucidates the potential mechanism by which lactylation promotes lipid accumulation under ND. Lactylation facilitates autophagy and protein degradation, leading to the recycling of carbon into the tricarboxylic acid (TCA) cycle, thereby providing carbon precursors for lipid synthesis. Additionally, lactylation induces the redirection of carbon from membrane lipids to TAG by upregulating lipases and enhancing the TCA cycle and β-oxidation pathways. This research offers a new perspective for the investigation of lipid biosynthesis in Nannochloropsis.

Workability of mRNA Sequencing for Predicting Protein Abundance

Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than proteomics methods, i.e., both mass spectrometry and immunochemical analysis. For this reason, most scientific studies are limited to assessing the level of mRNA content. At the same time, protein content (and its post-translational status) largely determines the cell's state and behavior. Such a forced extrapolation of conclusions from the transcriptome to the proteome often seems unjustified. The ratios of "transcript-protein" pairs can vary by several orders of magnitude for different genes. As a rule, the correlation coefficient between transcriptome-proteome levels for different tissues does not exceed 0.3-0.5. Several characteristics determine the ratio between the content of mRNA and protein: among them, the rate of movement of the ribosome along the mRNA and the number of free ribosomes in the cell, the availability of tRNA, the secondary structure, and the localization of the transcript. The technical features of the experimental methods also significantly influence the levels of the transcript and protein of the corresponding gene on the outcome of the comparison. Given the above biological features and the performance of experimental and bioinformatic approaches, one may develop various models to predict proteomic profiles based on transcriptomic data. This review is devoted to the ability of RNA sequencing methods for protein abundance prediction.

Transcriptome and Proteome Analysis Revealed That Hormone and Reactive Oxygen Species Synergetically Regulate Dormancy of Introgression Line in Rice (Oryza sativa L.)

Dormancy is a complex agronomy phenotype controlled by multiple signaling and a key trait repressing pre-harvest sprouting (PHS). However, the signaling network of dormancy remains unclear. In this study, we used Zhonghua11 (ZH11) with a weak dormancy, and Introgression line (IL) with a strong dormancy to study the mechanism of hormones and reactive oxygen species (ROS) crosstalk regulating rice dormancy. The germination experiment showed that the germination rate of ZH11 was 76.86%, while that of IL was only 1.25%. Transcriptome analysis showed that there were 1658 differentially expressed genes (DEGs) between IL and ZH11, of which 577 were up-regulated and 1081 were down-regulated. Additionally, DEGs were mainly enriched in oxidoreductase activity, cell periphery, and plant hormone signal transduction pathways. Tandem mass tags (TMT) quantitative proteomics analysis showed 275 differentially expressed proteins (DEPs) between IL and ZH11, of which 176 proteins were up-regulated, 99 were down-regulated, and the DEPs were mainly enriched in the metabolic process and oxidation-reduction process. The comprehensive transcriptome and proteome analysis showed that their correlation was very low, and only 56 genes were co-expressed. Hormone content detection showed that IL had significantly lower abscisic acid (ABA) contents than the ZH11 while having significantly higher jasmonic acid (JA) contents than the ZH11. ROS content measurement showed that the hydrogen peroxide (H₂O₂) content of IL was significantly lower than the ZH11, while the production rate of superoxide anion (O₂^.-) was significantly higher than the ZH11. These results indicate that hormones and ROS crosstalk to regulate rice dormancy. In particular, this study has deepened our mechanism of ROS and JA crosstalk regulating rice dormancy and is conducive to our precise inhibition of PHS.

Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress

Oil palm (Elaeis guineensis Jacq.) is an economically important tropical oil crop widely cultivated in tropical zones worldwide. Being a tropical crop, low-temperature stress adversely affects the oil palm. However, integrative leaf transcriptomic and proteomic analyses have not yet been conducted on an oil palm crop under cold stress. In this study, integrative omics transcriptomic and iTRAQ-based proteomic approaches were employed for three oil palm varieties, i.e., B × E (Bamenda × Ekona), O × G (E. oleifera × Elaeis guineensis), and T × E (Tanzania × Ekona), in response to low-temperature stress. In response to low-temperature stress at (8 °C) for 5 days, a total of 5175 up- and 2941 downregulated DEGs in BE-0_VS_BE-5, and a total of 3468 up- and 2443 downregulated DEGs for OG-0_VS_OG-5, and 3667 up- and 2151 downregulated DEGs for TE-0_VS_TE-5 were identified. iTRAQ-based proteomic analysis showed 349 up- and 657 downregulated DEPs for BE-0_VS_BE-5, 372 up- and 264 downregulated DEPs for OG-0_VS_OG-5, and 500 up- and 321 downregulated DEPs for TE-0_VS_TE-5 compared to control samples treated at 28 °C and 8 °C, respectively. The KEGG pathway correlation of oil palm has shown that the metabolic synthesis and biosynthesis of secondary metabolites pathways were significantly enriched in the transcriptome and proteome of the oil palm varieties. The correlation expression pattern revealed that TE-0_VS_TE-5 is highly expressed and BE-0_VS_BE-5 is suppressed in both the transcriptome and proteome in response to low temperature. Furthermore, numerous transcription factors (TFs) were found that may regulate cold acclimation in three oil palm varieties at low temperatures. Moreover, this study identified proteins involved in stresses (abiotic, biotic, oxidative, and heat shock), photosynthesis, and respiration in iTRAQ-based proteomic analysis of three oil palm varieties. The increased abundance of stress-responsive proteins and decreased abundance of photosynthesis-related proteins suggest that the TE variety may become cold-resistant in response to low-temperature stress. This study may provide a basis for understanding the molecular mechanism for the adaptation of oil palm varieties in response to low-temperature stress in China.

Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticus modulate epithelial cell turnover

A data-independent acquisition (DIA) assay library for targeted quantitation of thousands of Oreochromis niloticus gill proteins using a label- and gel-free workflow was generated and used to compare protein and mRNA abundances. This approach generated complimentary rather than redundant data for 1899 unique genes in gills of tilapia acclimated to freshwater and brackish water. Functional enrichment analyses identified mitochondrial energy metabolism, serine protease and immunity-related functions, and cytoskeleton/ extracellular matrix organization as major processes controlled by salinity in O. niloticus gills. Non-linearity in salinity-dependent transcriptome versus proteome regulation was revealed for specific functional groups of genes. The relationship was more linear for other molecular functions/ cellular processes, suggesting that the salinity-dependent regulation of O. niloticus gill function relies on post-transcriptional mechanisms for some functions/ processes more than others. This integrative systems biology approach can be adopted for other tissues and organisms to study cellular dynamics for many changing ecological contexts.

Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin

A transcriptome analysis reveals the transcripts and alleles differentially expressed in sugarcane genotypes with contrasting lignin composition. Sugarcane bagasse is a highly abundant resource that may be used as a feedstock for the production of biofuels and bioproducts in order to meet increasing demands for renewable replacements for fossil carbon. However, lignin imparts rigidity to the cell wall that impedes the efficient breakdown of the biomass into fermentable sugars. Altering the ratio of the lignin units, syringyl (S) and guaiacyl (G), which comprise the native lignin polymer in sugarcane, may facilitate the processing of bagasse. This study aimed to identify genes and markers associated with S/G ratio in order to accelerate the development of sugarcane bioenergy varieties with modified lignin composition. The transcriptome sequences of 12 sugarcane genotypes that contrasted for S/G ratio were compared and there were 2019 transcripts identified as differentially expressed (DE) between the high and low S/G ratio groups. These included transcripts encoding possible monolignol biosynthetic pathway enzymes, transporters, dirigent proteins and transcriptional and post-translational regulators. Furthermore, the frequencies of single nucleotide polymorphisms (SNPs) were compared between the low and high S/G ratio groups to identify specific alleles expressed with the phenotype. There were 2063 SNP loci across 787 unique transcripts that showed group-specific expression. Overall, the DE transcripts and SNP alleles identified in this study may be valuable for breeding sugarcane varieties with altered S/G ratio that may provide desirable bioenergy traits.

Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum

Tobacco (Nicotiana tabacum) pollen is a well-suited model for studying many fundamental biological processes owing to its well-defined and distinct development stages. It is also one of the major agents involved in the transmission of infectious viroids, which is the primary mechanism of viroid pathogenicity in plants. However, some viroids are non-transmissible and may be possibly degraded or eliminated during the gradual process of pollen development maturation. The molecular details behind the response of developing pollen against the apple fruit crinkle viroid (AFCVd) infection and viroid eradication is largely unknown. In this study, we performed an integrative analysis of the transcriptome and proteome profiles to disentangle the molecular cascade of events governing the three pollen development stages: early bicellular pollen (stage 3, S3), late bicellular pollen (stage 5, S5), and 6 h-pollen tube (PT6). The integrated analysis delivered the molecular portraits of the developing pollen against AFCVd infection, including mechanistic insights into the viroid eradication during the last steps of pollen development. The isobaric tags for label-free relative quantification (iTRAQ) with digital gene expression (DGE) experiments led us to reliably identify subsets of 5321, 5286, and 6923 proteins and 64,033, 60,597, and 46,640 expressed genes in S3, S5, and PT6, respectively. In these subsets, 2234, 2108 proteins and 9207 and 14,065 mRNAs were differentially expressed in pairwise comparisons of three stages S5 vs. S3 and PT6 vs. S5 of control pollen in tobacco. Correlation analysis between the abundance of differentially expressed mRNAs (DEGs) and differentially expressed proteins (DEPs) in pairwise comparisons of three stages of pollen revealed numerous discordant changes in mRNA/protein pairs. Only a modest correlation was observed, indicative of divergent transcription, and its regulation and importance of post-transcriptional events in the determination of the fate of early and late pollen development in tobacco. The functional and enrichment analysis of correlated DEGs/DEPs revealed the activation in pathways involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, and cofactor as well as vitamin metabolism, which points to the importance of these metabolic pathways in pollen development. Furthermore, the detailed picture of AFCVd-infected correlated DEGs/DEPs was obtained in pairwise comparisons of three stages of infected pollen. The AFCVd infection caused the modulation of several genes involved in protein degradation, nuclear transport, phytohormone signaling, defense response, and phosphorylation. Intriguingly, we also identified several factors including, DNA-dependent RNA-polymerase, ribosomal protein, Argonaute (AGO) proteins, nucleotide binding proteins, and RNA exonucleases, which may plausibly involve in viroid stabilization and eradication during the last steps of pollen development. The present study provides essential insights into the transcriptional and translational dynamics of tobacco pollen, which further strengthens our understanding of plant-viroid interactions and support for future mechanistic studies directed at delineating the functional role of candidate factors involved in viroid elimination.

Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain

Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities.

Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana

Nutrient limited conditions are common in natural phytoplankton communities and are often used to increase the yield of lipids from industrial microalgae cultivations. Here we studied the effects of bioavailable nitrogen (N) and phosphorus (P) deprivation on the proteome and transcriptome of the oleaginous marine microalga Nannochloropsis gaditana. Turbidostat cultures were used to selectively apply either N or P deprivation, controlling for variables including the light intensity. Global (cell-wide) changes in the proteome were measured using Tandem Mass Tag (TMT) and LC-MS/MS, whilst gene transcript expression of the same samples was quantified by Illumina RNA-sequencing. We detected 3423 proteins, where 1543 and 113 proteins showed significant changes in abundance in N and P treatments, respectively. The analysis includes the global correlation between proteomic and transcriptomic data, the regulation of subcellular proteomes in different compartments, gene/protein functional groups, and metabolic pathways. The results show that triacylglycerol (TAG) accumulation under nitrogen deprivation was associated with substantial downregulation of protein synthesis and photosynthetic activity. Oil accumulation was also accompanied by a diverse set of responses including the upregulation of diacylglycerol acyltransferase (DGAT), lipase, and lipid body associated proteins. Deprivation of phosphorus had comparatively fewer, weaker effects, some of which were linked to the remodeling of respiratory metabolism.

Immune responses to Bacillus thuringiensis in the midgut of the diamondback moth, Plutella xylostella

The diamondback moth, Plutella xylostella, is the first insect to develop resistance to Bacillus thuringiensis (Bt) in the field. To date, little is known about the molecular mechanism of the interaction between Bt and midgut immunity in P. xylostella. Here, we report immune responses in the P. xylostella midgut to Bt strain Bt8010 using a combined approach of transcriptomics and quantitative proteomics. Many genes in the Toll, IMD, JNK and JAK-STAT pathways and antimicrobial peptide genes were activated at 18 h post-infection. In the prophenoloxidase (PPO) cascade, four serpin genes were activated, and the PPO1 gene was suppressed by Bt8010. Inhibition of the two PPO proteins was observed at 18 h post-infection. Feeding Bt8010-infected larvae recombinant PPOs enhanced their survival. These results revealed that the Toll, IMD, JNK and JAK-STAT pathways were triggered and participated in the immune defence of the midgut against Bt8010, while the PPO cascade was inhibited and played an important role in this process.

Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean

BACKGROUND

Little is known about the molecular basis of seed size formation in endospermic seed of dicotyledons. The seed of castor bean (Ricinus communis L.) is considered as a model system in seed biology studies because of its persistent endosperms throughout seed development.

RESULTS

We compared the size of endosperm and endospermic cells between ZB107 and ZB306 and found that the larger seed size of ZB107 resulted from a higher cell count in the endosperm, which occupy a significant amount of the total seed volume. In addition, fresh weight, dry weight, and protein content of seeds were remarkably higher in ZB107 than in ZB306. Comparative proteomic and transcriptomic analyses were performed between large-seed ZB107 and small-seed ZB306, using isobaric tags for relative and absolute quantification (iTRAQ) and RNA-seq technologies, respectively. A total of 1416 protein species were identified, of which 173 were determined as differentially abundant protein species (DAPs). Additionally, there were 9545 differentially expressed genes (DEGs) between ZB306 and ZB107. Functional analyses revealed that these DAPs and DEGs were mainly involved in cell division and the metabolism of carbohydrates and proteins.

CONCLUSIONS

These findings suggest that both cell number and storage-component accumulation are critical for the formation of seed size, providing new insight into the potential mechanisms behind seed size formation in endospermic seeds.

iTRAQ proteomics reveals the regulatory response to Magnaporthe oryzae in durable resistant vs. susceptible rice genotypes

Rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most serious diseases. Although previous research using two-dimensional gel-based proteomics to assess the proteins related to the rice blast resistance had been done, few proteins were identified. Here, we used the iTRAQ method to detect the differentially expressed proteins (DEPs) in the durable resistant rice variety Gangyuan8 (GY8) and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to M. oryzae invasion, and then transcriptome sequencing was used to assist analysis A total of 193 and 672 DEPs were specifically identified in GY8 and LTH, respectively, with only 46 similarly expressed DEPs being shared by GY8 and LTH.39 DEPs involved in plant-pathogen interaction, plant hormone signal transduction, fatty acid metabolism and peroxisome biosynthesis were significantly different between compatible interaction (LTH) and incompatible interaction (GY8). Some proteins participated in peroxide signal transduction and biosynthesis was down-regulated in GY8 but up-regulated in LTH. A lot of genes encoding pathogenesis-related gene (PR), such as chitinase and glucanase, were significantly up-regulated at both the transcriptome and proteome levels at 24 hours post-inoculation in GY8, but up-regulated at the transcriptome level and down-regulated at the proteome level in LTH. Our study reveals that the pathogen-associated molecular pattern (PAMP)-triggered immunity defense system may be activated at the transcriptome level but was inhibited at the protein level in susceptible rice varieties after inoculation. The results may facilitate future studies of the molecular mechanisms of rice blast resistance.

Integrative omics analysis on phytohormones involved in oil palm seed germination

BACKGROUND

Heat treatment is widely used to break dormancy for seed germination and phytohormones could be deeply involved. However, effect of heat treatment on phytohormone related genes/proteins/metabolites and possible relationship with dormancy release remains unclear in oil palm. In this study, oil palm seeds were heat-treated at 39 °C for 60 days according to the method for commercial production. The embryos of seeds during heat treatment (0 d, 15 d, 30 d, 45 d and 60 d) and of germinated seeds (70 d and 75 d) were selected to discover the mechanisms involved in oil palm seed germination. RNA-seq and iTRAQ were applied to investigate DEGs and DEPs related to seed germination; qPCR and western blot were used as validation accordingly; endogenous phytohormones were determined by LC-MS/MS and exogenous phytohormones were also applied to validate their effects on seed germination.

RESULTS

RNA-seq results showed that plant hormone signal transduction was one of the most important pathways and eight phytohormones involved, while six of them (ABA, GA, ET, CTK, IAA and JA) were also identified by iTRAQ. Both RNA-seq and iTRAQ results showed that the expression of ABA decreased after heat treatment, which was further validated by qPCR and western blot. Furthermore, changes in endogenous phytohormones showed that ABA decreased rapidly to about 9% of the control at 30 d and then stayed at very low levels until germination; GA and CTK increased while IAA was not affected by heat treatment. Besides, exogenous ABA treatments (10, 100, 1000 mg/L) showed that the germination rate decreased to 63, 42 and 16% of the control, respectively, suggesting that ABA suppress seed germination and the inhibition effect increase with higher concentration; while the germination rates of exogenous GA and IAA treatments barely changed among different concentrations.

CONCLUSIONS

Phytohormones are deeply involved in oil palm seed germination and ABA acts as an inhibitor. Heat treatment can eliminate endogenous ABA and break dormancy, while GA and CTK may also involve in dormancy release. At least 30 days of heat treatment might be necessary. This study provided informative perspectives on oil palm seed germination, which could be also applicable in other palm species.

Study on Differential Protein Expression in Natural Selenium-Enriched and Non-Selenium-Enriched Rice Based on iTRAQ Quantitative Proteomics

This work was designated to scrutinize the protein differential expression in natural selenium-enriched and non-selenium-enriched rice using the Isobaric-tags for relative and absolute quantification (iTRAQ) proteomics approach. The extracted proteins were subjected to enzyme digestion, desalting, and identified by iTRAQ coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology. High pH C18 separation analysis was performed, and the data were then analyzed by Protein Pilot^TM (V4.5) search engine. Protein differential expression was searched out by comparing relatively quantified proteins. The analysis was conducted using gene ontology (GO), cluster of orthologous groups of proteins (COG) and Kyoto encyclopedia of genes and genomes (KEGG) metabolic pathways. A total of 3235 proteins were detected and 3161 proteins were quantified, of which 401 were differential proteins. 208 down-regulated and 193 up-regulated proteins were unveiled. 77 targeted significant differentially expressed proteins were screened out for further analysis, and were classified into 10 categories: oxidoreductases, transferases, isomerases, heat shock proteins, lyases, hydrolases, ligases, synthetases, tubulin, and actin. The results indicated that the anti-stress, anti-oxidation, active oxygen metabolism, carbohydrate and amino acid metabolism of natural selenium-enriched rice was higher than that of non-selenium rice. The activation of the starch synthesis pathway was found to be bounteous in non-selenium-enriched rice. Cysteine synthase (CYS) and methyltransferase (metE) might be the two key proteins that cause amino acid differences. OsAPx02, CatC, riPHGPX, HSP70 and HSP90 might be the key enzymes regulating antioxidant and anti-stress effect differences in two types of rice. This study provides basic information about deviations in protein mechanism and secondary metabolites in selenium-enriched and non-selenium-enriched rice.

Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening

Ethylene, the plant ripening hormone of climacteric fruit, is perceived by ethylene receptors which is the first step in the complex ethylene signal transduction pathway. Much progress has been made in elucidating the mechanism of this pathway, but there is still a lot to be done in the proteomic quantification of the main proteins involved, particularly during fruit ripening. This work focuses on the mass spectrometry based identification and quantification of the ethylene receptors (ETRs) and the downstream components of the pathway, CTR-like proteins (CTRs) and ETHYLENE INSENSITIVE 2 (EIN2). We used tomato as a model fruit to study changes in protein abundance involved in the ethylene signal transduction during fruit ripening. In order to detect and quantify these low abundant proteins located in the membrane of the endoplasmic reticulum, we developed a workflow comprising sample fractionation and MS analysis using parallel reaction monitoring. This work shows the feasibility of the identification and absolute quantification of all seven ethylene receptors, three out of four CTRs and EIN2 in four ripening stages of tomato. In parallel, gene expression was analyzed through real-time qPCR. Correlation between transcriptomic and proteomic profiles during ripening was only observed for three of the studied proteins, suggesting that the other signaling proteins are likely post-transcriptionally regulated. Based on our quantification results we were able to show that the protein levels of SlETR3 and SlETR4 increased during ripening, probably to control ethylene sensitivity. The other receptors and CTRs showed either stable levels that could sustain, or decreasing levels that could promote fruit ripening.

iTRAQ-Based Analysis of Proteins Co-Regulated by Brassinosteroids and Gibberellins in Rice Embryos during Seed Germination

Seed germination, a pivotal process in higher plants, is precisely regulated by various external and internal stimuli, including brassinosteroid (BR) and gibberellin (GA) phytohormones. The molecular mechanisms of crosstalk between BRs and GAs in regulating plant growth are well established. However, whether BRs interact with GAs to coordinate seed germination remains unknown, as do their common downstream targets. In the present study, 45 differentially expressed proteins responding to both BR and GA deficiency were identified using isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis during seed germination. The results indicate that crosstalk between BRs and GAs participates in seed germination, at least in part, by modulating the same set of responsive proteins. Moreover, most targets exhibited concordant changes in response to BR and GA deficiency, and gene ontology (GO) indicated that most possess catalytic activity and are involved in various metabolic processes. Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) analysis was used to construct a regulatory network of downstream proteins mediating BR- and GA-regulated seed germination. The mutation of GRP, one representative target, notably suppressed seed germination. Our findings not only provide critical clues for validating BR–GA crosstalk during rice seed germination, but also help to optimise molecular regulatory networks.

The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen

BACKGROUND

Pollen development is central for plant reproduction and is assisted by changes of the transcriptome and proteome. At the same time, pollen development and viability is largely sensitive to stress, particularly to elevated temperatures. The transcriptomic and proteomic changes during pollen development and of different stages in response to elevated temperature was targeted to define the underlying molecular principles.

RESULTS

The analysis of the transcriptome and proteome of Solanum lycopersicum pollen at tetrad, post-meiotic and mature stage before and after heat stress yielded a decline of the transcriptome but an increase of the proteome size throughout pollen development. Comparison of the transcriptome and proteome led to the discovery of two modes defined as direct and delayed translation. Here, genes of distinct functional processes are under the control of direct and delayed translation. The response of pollen to elevated temperature occurs rather at proteome, but not as drastic at the transcriptome level. Heat shock proteins, proteasome subunits, ribosomal proteins and eukaryotic initiation factors are most affected. On the example of heat shock proteins we demonstrate a decoupling of transcript and protein levels as well as a distinct regulation between the developmental stages.

CONCLUSIONS

The transcriptome and proteome of developing pollen undergo drastic changes in composition and quantity. Changes at the proteome level are a result of two modes assigned as direct and delayed translation. The response of pollen to elevated temperature is mainly regulated at the proteome level, whereby proteins related to synthesis and degradation of proteins are most responsive and might play a central role in the heat stress response of pollen.

Shape-Shifted Red Blood Cells: A Novel Red Blood Cell Stage?

Primitive nucleated erythroid cells in the bloodstream have long been suggested to be more similar to nucleated red cells of fish, amphibians, and birds than the red cells of fetal and adult mammals. Rainbow trout Ficoll-purified red blood cells (RBCs) cultured in vitro undergo morphological changes, especially when exposed to stress, and enter a new cell stage that we have coined shape-shifted RBCs (shRBCs). We have characterized these shRBCs using transmission electron microscopy (TEM) micrographs, Wright–Giemsa staining, cell marker immunostaining, and transcriptomic and proteomic evaluation. shRBCs showed reduced density of the cytoplasm, hemoglobin loss, decondensed chromatin in the nucleus, and striking expression of the B lymphocyte molecular marker IgM. In addition, shRBCs shared some features of mammalian primitive pyrenocytes (extruded nucleus surrounded by a thin rim of cytoplasm and phosphatidylserine (PS) exposure on cell surface). These shRBCs were transiently observed in heat-stressed rainbow trout bloodstream for three days. Functional network analysis of combined transcriptomic and proteomic studies resulted in the identification of proteins involved in pathways related to the regulation of cell morphogenesis involved in differentiation, cellular response to stress, and immune system process. In addition, shRBCs increased interleukin 8 (IL8), interleukin 1 β (IL1β), interferon ɣ (IFNɣ), and natural killer enhancing factor (NKEF) protein production in response to viral hemorrhagic septicemia virus (VHSV). In conclusion, shRBCs may represent a novel cell stage that participates in roles related to immune response mediation, homeostasis, and the differentiation and development of blood cells.

Proteomic analysis of xylem vessel cell differentiation in VND7-inducible tobacco BY-2 cells by two-dimensional gel electrophoresis

The xylem vessel is an essential structure for water conduction in vascular plants. Xylem vessel cells deposit thick secondary cell walls and undergo programmed cell death, to function as water-conducting elements. Since the discovery of the plant-specific NAC domain-type VASCULAR-RELATED NAC-DOMAIN (VND) transcription factors, which function as master switches of xylem vessel cell differentiation in Arabidopsis, much has been learned about the transcriptional regulatory network of xylem vessel cell differentiation. However, little is known about proteome dynamics during xylem vessel cell differentiation. Here, we performed two-dimensional electrophoresis-based proteomic analysis of xylem vessel cell differentiation using a transgenic tobacco BY-2 cell line carrying the VND7-inducible system (BY-2/35S::VND7-VP16-GR), in which synchronous trans-differentiation into xylem vessel cells can be induced by the application of a glucocorticoid. Of the 47 spots revealed by gel electrophoresis, we successfully identified 40 proteins. Seventeen proteins, including several well-characterized proteins such as a cysteine protease and serine carboxypeptidase (involved in programmed cell death), were upregulated after 24 h of induction. However, previous transcriptomic analysis showed that only eight of these proteins are upregulated at the transcriptional level during xylem vessel cell differentiation in BY-2/35S::VND7-VP16-GR cells. These findings suggest that post-transcriptional regulation strongly affects proteomic dynamics during xylem vessel cell differentiation.

Proteomic analysis of Camellia sinensis (L.) reveals a synergistic network in the response to drought stress and recovery

Drought is a crucial limiting factor for tea yield and quality. To systematically characterize the molecular response of tea plants to drought stress and its capacity to recover, we used iTRAQ-based comparative proteomic approach to investigate the effects of drought on protein expression profiles in tea seedlings subjected to different drought treatments. A total of 3274 proteins were identified, of which 2169 and 2300 showed differential expressions during drought and recovery, respectively. Functional annotation showed that multiple biological processes were regulated, suggesting that tea plants probably employed multiple and synergistic resistance mechanisms in dealing with drought stress. Hierarchical clustering showed that chlorophyll a/b-binding proteins were up-regulated in DB and RE, suggesting that tea plants might regulate expression of chlorophyll a/b-binding proteins to maintain the photosystem II function during drought stress. Abundant proteins involved in sulfur-containing metabolite pathways, such as glutathione, taurine, hypotaurine, methionine, and cysteine, changed significantly during drought stress. Among them, TL29 interacted with LHCb6 to connect S-containing metabolites with chlorophyll a/b-binding proteins. This suggests that sulfur-containing compounds play important roles in the response to drought stress in tea plants. In addition, the expression of PAL was up-regulated in DA and down-regulated in DB. Cinnamyl alcohol dehydrogenase, caffeic acid O-methyltransferase, and 4-coumarate-CoA ligase also showed significant changes in expression levels, which regulated the biosynthesis of polyphenols. The results indicate that slight drought stress might promote polyphenol biosynthesis, while serious drought stress leads to inhibition. The expression of lipoxygenase and short-chain dehydrogenase increased during slight drought stress and some volatile metabolite pathways were enriched, indicating that drought stress might affect the tea aroma. The study provides valuable information that will lay the foundation for studies investigating the functions of drought response genes in tea leaves.

Enhancing crop yield by optimizing plant developmental features

A number of plant features and traits, such as overall plant architecture, leaf structure and morphological features, vascular architecture and flowering time are important determinants of photosynthetic efficiency and hence the overall performance of crop plants. The optimization of such developmental traits thus has great potential to increase biomass and crop yield. Here, we provide a comprehensive review of these developmental traits in crop plants, summarizing their genetic regulation and highlighting the potential of manipulating these traits for crop improvement. We also briefly review the effects of domestication on the developmental features of crop plants. Finally, we discuss the potential of functional genomics-based approaches to optimize plant developmental traits to increase yield.

Proteomic Analysis of Differences in Fiber Development between Wild and Cultivated Gossypium hirsutum L

Upland cotton (Gossypium hirsutum L.) is one of the world's most important fiber crops, accounting for more than 90% of all cotton production. While their wild progenitors have relatively short and coarse, often tan-colored fibers, modern cotton cultivars possess longer, finer, stronger, and whiter fiber. In this study, the wild and cultivated cottons (YU-3 and TM-1) selected show significant differences on fibers at 10 days postanthesis (DPA), 20 DPA, and mature stages at the morphological level. To explore the effects of domestication, reveal molecular mechanisms underlying these phenotypic differences, and better inform our efforts to further enhance cotton fiber quality, isobaric tags for relative and absolute protein quantification-facilitated proteomic methods were performed on developing fibers. There were 6990 proteins identified; among them, 336 were defined as differentially expressed proteins between fibers of wild versus domesticated cotton. The down- or up-regulated proteins in wild cotton were involved in phenylpropanoid biosynthesis, zeatin biosynthesis, fatty acid elongation, and other processes. Association analysis between transcriptome and proteome showed positive correlations between transcripts and proteins at both 10 DPA and 20 DPA. Differences in proteomics have been verified at the mRNA level by quantitative real-time polymerase chain reaction and have been validated at the physiological and biochemical levels by POD (peroxidase) activity assays and ZA (zeatin) content estimates. This work corroborates the major pathways involved in cotton fiber development and demonstrates that POD activity and zeatin content have a great potential related to fiber elongation and thickening.

Comparative proteomic analysis of autotetraploid and diploid Paulownia tomentosa reveals proteins associated with superior photosynthetic characteristics and stress adaptability in autotetraploid Paulownia

To enlarge the germplasm resource of Paulownia plants, we used colchicine to induce autotetraploid Paulownia tomentosa, as reported previously. Compared with its diploid progenitor, autotetraploid P. tomentosa exhibits better photosynthetic characteristics and higher stress resistance. However, the underlying mechanism for its predominant characteristics has not been determined at the proteome level. In this study, isobaric tag for relative and absolute quantitation coupled with liquid chromatography-tandem mass spectrometry was employed to compare proteomic changes between autotetraploid and diploid P. tomentosa. A total of 1427 proteins were identified in our study, of which 130 proteins were differentially expressed between autotetraploid and diploid P. tomentosa. Functional analysis of differentially expressed proteins revealed that photosynthesis-related proteins and stress-responsive proteins were significantly enriched among the differentially expressed proteins, suggesting they may be responsible for the photosynthetic characteristics and stress adaptability of autotetraploid P. tomentosa. The correlation analysis between transcriptome and proteome data revealed that only 15 (11.5%) of the differentially expressed proteins had corresponding differentially expressed unigenes between diploid and autotetraploid P. tomentosa. These results indicated that there was a limited correlation between the differentially expressed proteins and the previously reported differentially expressed unigenes. This work provides new clues to better understand the superior traits in autotetraploid P. tomentosa and lays a theoretical foundation for developing Paulownia breeding strategies in the future.

Dissection of brassinosteroid-regulated proteins in rice embryos during germination by quantitative proteomics

Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice. In the present study, we used isobaric tags for relative and absolute quantification (iTRAQ) based proteomic approach to study BR-regulated proteome during the early stage of seed germination. The results showed that more than 800 BR-responsive proteins were identified, including 88 reliable target proteins responsive to stimuli of both BR-deficiency and BR-insensitivity. Moreover, 90% of the 88 target proteins shared a similar expression change pattern. Gene ontology and string analysis indicated that ribosomal structural proteins, as well as proteins involved in protein biosynthesis and carbohydrate metabolisms were highly clustered. These findings not only enrich BR-regulated protein database in rice seeds, but also allow us to gain novel insights into the molecular mechanism of BR regulated seed germination.