iTRAQ-based proteomic analysis of fertile and sterile flower buds from a genetic male sterile line ‘AB01’ in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

Unveiling molecular mechanisms of pepper resistance to Phytophthora capsici through grafting using iTRAQ-based proteomic analysis

Phytophthora blight severely threatens global pepper production. Grafting bolsters plant disease resistance, but the underlying molecular mechanisms remain unclear. In this study, we used P. capsici-resistant strain 'ZCM334' and susceptible strain 'Early Calwonder' for grafting. Compared to self-rooted 'Early Calwonder' plants, 'ZCM334' grafts exhibited delayed disease onset, elevated resistance, and reduced leaf cell damage, showcasing the potential of grafting in enhancing pepper resistance to P. capsici. Proteomic analysis via the iTRAQ technology unveiled 478 and 349 differentially expressed proteins (DEPs) in the leaves and roots, respectively, between the grafts and self-rooted plants. These DEPs were linked to metabolism and cellular processes, stimulus responses, and catalytic activity and were significantly enriched in the biosynthesis of secondary metabolites, carbon fixation in photosynthetic organizations, and pyruvate metabolism pathways. Twelve DEPs exhibiting consistent expression trends in both leaves and roots, including seven related to P. capsici resistance, were screened. qRT-PCR analysis confirmed a significant correlation between the protein and transcript levels of DEPs after P. capsici inoculation. This study highlights the molecular mechanisms whereby grafting enhances pepper resistance to Phytophthora blight. Identification of key genes provides a foundation for studying the regulatory network governing the resistance of pepper to P. capsici.

Integrated transcriptome and proteome analysis provides insights into the mechanism of cytoplasmic male sterility (CMS) in tobacco (Nicotiana tabacum L.)

Cytoplasmic male sterility (CMS) is critical in maximizing crop yield and quality by utilizing tobacco heterosis. However, the mechanism of tobacco CMS formation remains unknown. Using paraffin section observation, transcriptome sequencing, and TMT proteomic analysis, this study describes the differences in expression profiles in morphology, transcription, and translation between the sua-CMS tobacco line (MSYY87) and its corresponding maintainer line (YY87). According to the microspore morphology, MSYY87 began to exhibit abnormal microspore development during the early stages of germination and differentiation (androgynous primordium differentiation stage). According to transcriptomic and proteomic analyses, 17 genes/proteins involved in lipid transport/binding and phenylpropane metabolism were significantly down-regulated at both the mRNA and protein levels. Through further analysis, we identified some key genes that may be involved in tobacco male sterility, including β-GLU related to energy metabolism, 4CL and bHLHs related to anther wall formation, nsLTPs related to pollen germination and anther cuticle, and bHLHs related to pollen tapetum degradation. We speculate that the down-regulation of these genes affects the normal physiological metabolism, making tobacco plants show male sterility. SIGNIFICANCE: Cytoplasmic male sterility (CMS) plays a vital role in utilizing tobacco heterosis and enhancing crop yield and quality. We observed paraffin sections and conducted transcriptome sequencing and mitochondrial proteomics to examine the tobacco CMS line Yunyan 87 (MSYY87) and its maintainer line Yunyan 87 (YY87). The down-regulation expression of β-GLU resulted in insufficient ATP supply, which resulted in disordered energy metabolism. The down-regulation expression of 4CL, nsLTPs and bHLHs may affect the formation of anther wall and anther cuticle, pollen germination, as well as the degradation of pollen tapetum. These various abnormal physiological processes, the male sterility of tobacco is finally caused. The findings shed light on the molecular mechanisms of tobacco CMS and serve as a model for fertility research in other flowering plants.

Understanding the Proteomes of Plant Development and Stress Responses in Brassica Crops

Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achieved in the past decade, the methods to understand molecular mechanisms underlying the traits of interest have also taken a sharp upturn in plant breeding practices. Proteomics has emerged as one of the preferred choices nowadays along with genomics and other molecular approaches, as proteins are the ultimate effector molecules responsible for phenotypic changes in living systems, and allow plants to resist variable environmental stresses. In the last two decades, rapid progress has been made in the field of proteomics research in Brassica crops, but a comprehensive review that collates the different studies is lacking. This review provides an inclusive summary of different proteomic studies undertaken in Brassica crops for cytoplasmic male sterility, oil content, and proteomics of floral organs and seeds, under different biotic and abiotic stresses including post-translational modifications of proteins. This comprehensive review will help in understanding the role of different proteins in controlling plant phenotypes, and provides information for initiating future studies on Brassica breeding and improvement programs.

Transcriptomic and iTRAQ-Based Quantitative Proteomic Analyses of inap CMS in Brassica napus L

Brassica napus inap cytoplasmic male sterility (CMS) is a novel sterile line with potential application in rapeseed hybrid breeding. Sterile cytoplasm was obtained from Isatis indigotica through somatic fusion and then recurrent backcrossing with B. napus. Previous studies have shown that inap CMS abortion occurred before the stamen primordia (stage 4–5), but the genetic mechanism of sterility needs to be studied. RNA-seq analyses were performed on the floral buds at two stages (0–5 and 6–8), before and after the formation of stamen primordium. As a result, a total of 1769 and 594 differentially expressed genes (DEGs) were detected in the CMS line compared to its maintainer line at the two stages, respectively. In accordance with the CMS phenotype, the up- and downstream regulators of the stamen identity genes AP3 and PI were up- and downregulated in the CMS line, respectively. Furthermore, isobaric tags for relative and absolute quantitation (iTRAQ) analysis showed that a total of 760 differentially abundant proteins (DAPs) were identified in flower buds at stages 0–8, and most of the proteins related to the anther development, oxidative phosphorylation, and programmed cell death (PCD) were downregulated in inap CMS. In combined transcriptomic and proteomic analysis, a total of 32 DEGs/DAPs were identified, of which 7 common DEGs/DAPs had the same expression trend at stage 0–8 of flower development. The downregulation of genes related to the energy deficiency, hormone signal transduction, and the maintenance of mitochondrial metabolic homeostasis at stage 0–5 might disturb the normal differentiation of stamen primordium, resulting in carpelloid stamen of inap CMS. The study will help provide insights into the molecular mechanism of this new male sterility.

Proteomic and Phosphoproteomic Analyses Reveal a Complex Network Regulating Pollen Abortion and Potential Candidate Proteins in TCMS Wheat

Thermosensitive sterile lines are natural materials for exploring the effects of anther development on male fertility. To study the possible molecular mechanisms regulating protein activity during the induction of male sterility, proteomic and phosphoproteomic analyses with tandem mass tags (TMTs) were used to study the binucleate anther of the thermosensitive sterile wheat line YS3038. A total of 9072 proteins, including 5019 phosphoproteins, were identified. Enrichment analyses of differentially abundant proteins (DAPs) and phosphoproteins (DAPPs) in metabolic pathways showed that both were mainly related to energy metabolism. Soluble sugar and ATP content were significantly decreased, free fatty acid content was significantly increased, and ROS was abnormally accumulated in male sterile YS3038-A. In addition, 233 kinase–substrate pairs involved in potential phosphorylation control networks were predicted to regulate fertility. Candidate proteins were identified, and a quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to validate the TMT results. TaPDCD5 is likely to be involved in fertility conversion of YS3038 by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS). Our data provide new insights into the mechanism of TCMS, which has value for identifying potential candidate proteins associated with the formation or abortion of pollen and promotion of wheat heterosis utilization.

Integrative Analyses of Transcriptomics and Metabolomics in Sex Differentiation of Mulberry Flowers

Sex determination and sex differentiation of plants are important physiological processes of plant development. Mulberry (Morus indica L.) is an important economic tree being cultivated in sericulture countries, and mulberry leaf is commonly used for sericulture. The transcriptomic and metabolomic differences between the staminate flowers (SFs) and pistillate flowers (PFs) of mulberry were investigated by RNA sequencing and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Overall, we uncovered 4,230 genes and 209 metabolites are significantly differentially expressed between the SFs and PFs of mulberry. The combined transcriptomic and metabolomic analysis revealed these differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) are involved in flavonoid biosynthesis, galactose metabolism, plant–pathogen interaction, and starch and sucrose metabolism, and these detected DEGs and DEMs may be associated with sex differentiation of mulberry through the regulation of the enrichment pathways, such as the MAPK pathway, flavonoid biosynthesis, galactose metabolism, plant–pathogen interaction, and starch and sucrose metabolism. This study will provide a rich source for the analysis of the molecular mechanism of mulberry sex differentiation processes.

TMT-based comparative proteomic analysis of the male-sterile mutant ms01 sheds light on sporopollenin production and pollen development in wucai (Brassica campestris L.)

A spontaneous male-sterile mutant ms01 was discovered from the excellent high-generation inbred line 'hx12-6-3' in wucai. Compared with wild-type 'hx12-6-3', ms01 displayed complete male sterility with degenerated stamens and no pollen. In this study, cytological observation revealed that the tapetum of the anthers of ms01 had degraded in advance, and microspore development had stagnated in the mononuclear stage, ultimately resulting in completely aborted pollen. Genetic analysis indicated that the sterility of ms01 was controlled by a single recessive nuclear gene. In the differential proteomic analysis of 'hx12-6-3' and ms01 flower buds using a tandem mass tags-based approach, a comparison of two stages (stage a and stage e) revealed 1272 differentially abundant proteins (DAPs). The abnormal variation of the anther cuticle, pollen coat, and sporopollenin production were effected by lipid metabolism and phenylpropanoid biosynthesis in the mutant ms01. Further analysis elucidated that pollen development was associated with amino acid metabolism, protein synthesis and degradation, carbohydrate metabolism, flavonoid biosynthesis and glutathione metabolism. These results provide novel insights into the molecular mechanism of GMS (genic male sterility) in wucai. SIGNIFICANCE: ms01, as the first indentified spontaneous male-sterile mutant in wucai, plays a significant role in the initial study of GMS (genic male sterility). In our study, the key DAPs related to anther and pollen development were obtained by TMT-based comparative proteomic analysis. We found that the abnormal accumulation of H₂O₂ might induce premature degradation of the tapetum, causing anther metabolism disorder and pollen abortion. This process involved multiple DAPs and formed a complex regulatory network that generated a series of physiological metabolic alterations, ultimately leading to male sterility. Our results provide a theoretical foundation for further research on the complex anther and pollen development process.

Multiomics Analyses of Two Sorghum Cultivars Reveal the Molecular Mechanism of Salt Tolerance

Sorghum [Sorghum bicolor (L.) Moench] is one of the most important cereal crops and contains many health-promoting substances. Sorghum has high tolerance to abiotic stress and contains a variety of flavonoids compounds. Flavonoids are produced by the phenylpropanoid pathway and performed a wide range of functions in plants resistance to biotic and abiotic stress. A multiomics analysis of two sorghum cultivars (HN and GZ) under different salt treatments time (0, 24, 48, and 72) was performed. A total of 45 genes, 58 secondary metabolites, and 246 proteins were recognized with significant differential abundances in different comparison models. The common differentially expressed genes (DEGs) were allocated to the "flavonoid biosynthesis" and "phenylpropanoid biosynthesis" pathways. The most enriched pathways of the common differentially accumulating metabolites (DAMs) were "flavonoid biosynthesis," followed by "phenylpropanoid biosynthesis" and "arginine and proline metabolism." The common differentially expressed proteins (DEPs) were mainly distributed in "phenylpropanoid biosynthesis," "biosynthesis of cofactors," and "RNA transport." Furthermore, considerable differences were observed in the accumulation of low molecular weight nonenzymatic antioxidants and the activity of antioxidant enzymes. Collectively, the results of our study support the idea that flavonoid biological pathways may play an important physiological role in the ability of sorghum to withstand salt stress.

Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera

Camellia oleifera (C. oleifera) is one of the four major woody oil-bearing crops in the world and has relatively high ecological, economic, and medicinal value. Its seeds undergo a series of complex physiological and biochemical changes during ripening, which is mainly manifested as the accumulation and transformation of certain metabolites closely related to oil quality, especially flavonoids and fatty acids. To obtain new insights into the underlying molecular mechanisms, a parallel analysis of the transcriptome and proteome profiles of C. oleifera seeds at different maturity levels was conducted using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ) complemented with gas chromatography-mass spectrometry (GC-MS) data. A total of 16,530 transcripts and 1228 proteins were recognized with significant differential abundances in pairwise comparisons of samples at various developmental stages. Among these, 317 were coexpressed with a poor correlation, and most were involved in metabolic processes, including fatty acid metabolism, α-linolenic acid metabolism, and glutathione metabolism. In addition, the content of total flavonoids decreased gradually with seed maturity, and the levels of fatty acids generally peaked at the fat accumulation stage; these results basically agreed with the regulation patterns of genes or proteins in the corresponding pathways. The expression levels of proteins annotated as upstream candidates of phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) as well as their cognate transcripts were positively correlated with the variation in the flavonoid content, while shikimate O-hydroxycinnamoyltransferase (HCT)-encoding genes had the opposite pattern. The increase in the abundance of proteins and mRNAs corresponding to alcohol dehydrogenase (ADH) was associated with a reduction in linoleic acid synthesis. Using weighted gene coexpression network analysis (WGCNA), we further identified six unique modules related to flavonoid, oil, and fatty acid anabolism that contained hub genes or proteins similar to transcription factors (TFs), such as MADS intervening keratin-like and C-terminal (MIKC_MADS), type-B authentic response regulator (ARR-B), and basic helix-loop-helix (bHLH). Finally, based on the known metabolic pathways and WGCNA combined with the correlation analysis, five coexpressed transcripts and proteins composed of cinnamyl-alcohol dehydrogenases (CADs), caffeic acid 3-O-methyltransferase (COMT), flavonol synthase (FLS), and 4-coumarate: CoA ligase (4CL) were screened out. With this exploratory multiomics dataset, our results presented a dynamic picture regarding the maturation process of C. oleifera seeds on Hainan Island, not only revealing the temporal specific expression of key candidate genes and proteins but also providing a scientific basis for the genetic improvement of this tree species.

The impaired biosynthetic networks in defective tapetum lead to male sterility in watermelon

Heterosis has been widely applied in watermelon breeding, because of the higher resistance and yield of hybrid. As the basis of heterosis utilization, genic male sterility (GMS) is an important tool for facilitating hybrid seed production, while the detailed mechanism in watermelon is still largely unknown. Here, we report a spontaneous mutant Se18 exhibited complete male sterility due to the uniquely multilayered tapetum and the un-meiotic pollen mother cells during pollen development. Using TMT based quantitative proteomic analyses, a total of 348 differentially abundant proteins (DAPs) were detected with the overwhelming majority down-regulated in mutant Se18. By analyzing the putative orthologs/homologs of Arabidopsis GMS related genes, the biosynthesis and transport of sporopollenin and tryphine precursors were predictably altered in mutant compared to its sibling wild type. Moreover, the general phenylpropanoid pathway as well as its related metabolisms was also expectably impaired in mutant, coincident with the pale yellow petals. Notably, some key transcriptional factors regulating tapetum development, together with their down-regulated targets, offered potentially valuable candidates regarding of male sterility. Collectively, the disrupted regulatory networks underlying male sterility of watermelon was proposed, which provide novel insights into genetic mechanism of male reproductive process and rich gene resources for future research. SIGNIFICANCE: Watermelon is an importantly economical cucurbit crop worldwide, with high nutritional value. Although several male sterile mutants have been identified in watermelon, the underlying molecular mechanism is poorly elucidated. Comparative cytological analysis revealed that the defective development of tapetum was responsible for male sterility in mutant Se18. Combined with the morphological comparison, male floral buds at 2.0-2.5 mm in diameter were confirmed with no obvious phenotypic differences but distinct cytological defects, which were in turn sampled for TMT based proteomic analyses. Referring to functionally characterized GMS related genes, the genetic pathway DYT1-TDF1-AMS-MS188-MS1 regulating tapetum development, together with some downstream targets, were considerably altered in mutant Se18. Moreover, enrichment analyses illustrated the general phenylpropanoid related metabolisms, as well as the biosynthesis and transport of sporopollenin and tryphine precursors, were significantly disrupted in defective anther development. Collectively, the proposed regulatory networks in watermelon not only contribute to a better understanding of molecular mechanisms underlying male sterility, but also provide valuable GMS related candidates for future researches.

High-generation near-isogenic lines combined with multi-omics to study the mechanism of polima cytoplasmic male sterility

BACKGROUND

Cytoplasmic male sterility (CMS), which naturally exists in higher plants, is a useful mechanism for analyzing nuclear and mitochondrial genome functions and identifying the role of mitochondrial genes in the plant growth and development. Polima (pol) CMS is the most universally valued male sterility type in oil-seed rape. Previous studies have described the pol CMS restorer gene Rfp and the sterility-inducing gene orf224 in oil-seed rape, located in mitochondria. However, the mechanism of fertility restoration and infertility remains unknown. Moreover, it is still unknown how the fecundity restorer gene interferes with the sterility gene, provokes the sterility gene to lose its function, and leads to fertility restoration.

RESULT

In this study, we used multi-omics joint analysis to discover candidate genes that interact with the sterility gene orf224 and the restorer gene Rfp of pol CMS to provide theoretical support for the occurrence and restoration mechanisms of sterility. Via multi-omics analysis, we screened 24 differential genes encoding proteins related to RNA editing, respiratory electron transport chain, anther development, energy transport, tapetum development, and oxidative phosphorylation. Using a yeast two-hybrid assay, we obtained a total of seven Rfp interaction proteins, with orf224 protein covering five interaction proteins.

CONCLUSIONS

We propose that Rfp and its interacting protein cleave the transcript of atp6/orf224, causing the infertility gene to lose its function and restore fertility. When Rfp is not cleaved, orf224 poisons the tapetum cells and anther development-related proteins, resulting in pol CMS mitochondrial dysfunction and male infertility. The data from the joint analysis of multiple omics provided information on pol CMS's potential molecular mechanism and will help breed B. napus hybrids.

Transcriptomic and proteomic analyses of a new cytoplasmic male sterile line with a wild Gossypium bickii genetic background

Background

Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge,

no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conjoint transcriptomic and proteomic analysis was first performed between Yamian A and its maintainer Yamian B.

Results

We detected 550 differentially expressed transcript-derived fragments (TDFs) and at least 1013 proteins in anthers at various developmental stages. Forty-two TDFs and 11 differentially expressed proteins (DEPs) were annotated by analysis in the genomic databases of G. austral, G. arboreum and G. hirsutum. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to better understand the functions of these TDFs and DEPs. Transcriptomic and proteomic results showed that UDP-glucuronosyl/UDP-glucosyltransferase, 60S ribosomal protein L13a-4-like, and glutathione S-transferase were upregulated; while heat shock protein Hsp20, ATPase, F0 complex, and subunit D were downregulated at the microspore abortion stage of Yamian A. In addition, several TDFs from the transcriptome and several DEPs from the proteome were detected and confirmed by quantitative real-time PCR as being expressed in the buds of seven different periods of development. We established the databases of differentially expressed genes and proteins between Yamian A and its maintainer Yamian B in the anthers at various developmental stages and constructed an interaction network based on the databases for a comprehensive understanding of the mechanism underlying CMS with a wild cotton genetic background.

Conclusion

We first analyzed the molecular mechanism of CMS Yamian A from the perspective of omics, thereby providing an experimental basis and theoretical foundation for future research attempting to analyze the abortion mechanism of new CMS with a wild Gossypium bickii background and to realize three-line matching.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07261-y.

An Integrative Analysis of Transcriptome, Proteome and Hormones Reveals Key Differentially Expressed Genes and Metabolic Pathways Involved in Flower Development in Loquat

Flower development is a vital developmental process in the life cycle of woody perennials, especially fruit trees. Herein, we used transcriptomic, proteomic, and hormone analyses to investigate the key candidate genes/proteins in loquat (Eriobotrya japonica) at the stages of flower bud differentiation (FBD), floral bud elongation (FBE), and floral anthesis (FA). Comparative transcriptome analysis showed that differentially expressed genes (DEGs) were mainly enriched in metabolic pathways of hormone signal transduction and starch and sucrose metabolism. Importantly, the DEGs of hormone signal transduction were significantly involved in the signaling pathways of auxin, gibberellins (GAs), cytokinin, ethylene, abscisic acid (ABA), jasmonic acid, and salicylic acid. Meanwhile, key floral integrator genes FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and floral meristem identity genes SQUAMOSA PROMOTER BINDING LIKE (SPL), LEAFY (LFY), APETALA1 (AP1), and AP2 were significantly upregulated at the FBD stage. However, key floral organ identity genes AGAMOUS (AG), AP3, and PISTILLATA (PI) were significantly upregulated at the stages of FBE and FA. Furthermore, transcription factors (TFs) such as bHLH (basic helix-loop-helix), NAC (no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF1/2) and cup-shaped cotyledon (CUC2)), MYB_related (myeloblastosis_related), ERF (ethylene response factor), and C2H2 (cysteine-2/histidine-2) were also significantly differentially expressed. Accordingly, comparative proteomic analysis of differentially accumulated proteins (DAPs) and combined enrichment of DEGs and DAPs showed that starch and sucrose metabolism was also significantly enriched. Concentrations of GA3 and zeatin were high before the FA stage, but ABA concentration remained high at the FA stage. Our results provide abundant sequence resources for clarifying the underlying mechanisms of the flower development in loquat.

Gibberellin recovers seed germination in rice with impaired brassinosteroid signalling

Seed germination is essential for ensuring grain yield and quality. Germination rate, uniformity, and post-germination growth all contribute to cultivation. Although the phytohormones gibberellin (GA) and brassinosteroid (BR) are known to regulate germination, the underlying mechanism of their crosstalk in co-regulating rice seed germination remains unclear. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) proteomic approach was employed to identify target proteins responsive to GA during recovery of germination in BR-deficient and BR-insensitive rice. A total of 42 differentially abundant proteins were identified in both BR-deficient and BR-insensitive plants, and most were altered consistently in the two groups. Gene Ontology (GO) analysis revealed enrichment in proteins with binding and catalytic activity. A potential protein-protein interaction network was constructed using STRING analysis, and five Late Embryogenesis Abundant (LEA) family members were markedly down-regulated at both mRNA transcript and protein levels. These LEA genes were specifically expressed in rice seeds, especially during the latter stages of seed development. Mutation of LEA33 affected rice grain size and seed germination, possibly by reducing BR accumulation and enhancing GA biosynthesis. The findings improve our knowledge of the mechanisms by which GA and BR coordinate seed germination.

Complementary transcriptome and proteome profiling in the mature seeds of Camellia oleifera from Hainan Island

Camellia oleifera Abel. (C. oleifera), as an important woody tree species producing edible oils in China, has attracted enormous attention due to its abundant unsaturated fatty acids and their associated benefits to human health. To reveal novel insights into the characters during the maturation period of this plant as well as the molecular basis of fatty acid biosynthesis and degradation, we conducted a conjoint analysis of the transcriptome and proteome of C. oleifera seeds from Hainan Island. Using RNA sequencing (RNA-seq) technology and shotgun proteomic method, 59,391 transcripts and 40,500 unigenes were obtained by TIGR Gene Indices Clustering Tools (TGICL), while 1691 protein species were identified from Mass Spectrometry (MS). Subsequently, all genes and proteins were employed in euKaryotic Orthologous Groups (KOG) classification, Gene Ontology (GO) annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to investigate their essential functions. The results indicated that the most abundant pathways were biological metabolic processes. There were 946 unigenes associated with lipid metabolism at the transcriptome level, with 116 proteins at the proteome level; among these, 38 specific proteins were involved in protein-protein interactions, with the majority being related to fatty acid catabolic process. The expression levels of 21 candidate unigenes encoding target proteins were further detected by quantitative real-time polymerase chain reaction (qRT-PCR). Finally, Gas Chromatography Mass Spectrometry (GC-MS) was carried out to determine the fatty acid composition of C. oleifera oil. These findings not only deepened our understanding about the molecular mechanisms of fatty acid metabolism but also offered new evidence concerning the roles of relevant proteins in oil-bearing crops. Furthermore, the lipid-associated proteins recognized in this research might be helpful in providing a reference for the synthetic regulation of C. oleifera oil quality by genetic engineering techniques, thus resulting in potential application in agriculture.

iTRAQ-Based Quantitative Proteomics Analysis of HeLa Cells Infected With Chlamydia muridarum TC0668 Mutant and Wild-Type Strains

Chlamydia muridarum, an obligate intracellular pathogen, was used to establish a murine model of female upper genital tract infection by Chlamydia trachomatis. TC0668 in C. muridarum is a hypothetical chromosomal virulence protein that is involved in upper genital tract pathogenesis. The infection of mice with the C. muridarum TC0668-mutant (G216*) strain results in less pathological damage in the upper genital tract. In this study, an isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics analysis was performed to identify differentially expressed proteins between TC0668 wild-type (TC0668^wt) and TC0668 mutant (TC0668^mut) strains at 6, 12, 18, and 24 h post-infection (p.i.). Of the 550 proteins differentially expressed at 18 h p.i., 222 and 328 were up-regulated and down-regulated, respectively, inTC0668^mut-infected cells. The expression of seven up-regulated proteins (encoded by SRPRB, JAK1, PMM1, HLA-DQB1, THBS1, ITPR1, and BCAP31) and three down-regulated proteins (encoded by MAPKAPK2, TRAFD1, and IFI16) from the iTRAQ analysis were validated using quantitative real-time (qRT)-PCR. The qRT-PCR results were consistent with those of iTRAQ. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the differentially expressed proteins primarily participated in inflammatory responses, fibrosis, metabolic processes, and complement coagulation cascades, and were mainly enriched in the phosphatidylinositol 3′-kinase (PI3K)/Akt, nuclear factor kappa-B (NF-κB), and other signaling pathways. Using western-blotting and immunofluorescence detection, significant differences in activation of the PI3K/Akt and NF-κB signaling pathways were observed between the TC0668^wt- and TC0668^mut-infected cells. Differentially expressed proteins linked with inflammation and fibrosis were used in a protein-protein interaction network analysis. The results suggest that TC0668 may play a pivotal role in C. muridarum-induced genital pathology by inducing inflammatory responses and fibrosis, which may involve the activation of the PI3K/Akt and NF-κB signaling pathways.