Differential proteomics analysis to identify proteins and pathways associated with male sterility of soybean using iTRAQ-based strategy

Advances in CRISPR/Cas9-based research related to soybean [Glycine max (Linn.) Merr] molecular breeding

Soybean [Glycine max (Linn.) Merr] is a source of plant-based proteins and an essential oilseed crop and industrial raw material. The increase in the demand for soybeans due to societal changes has coincided with the increase in the breeding of soybean varieties with enhanced traits. Earlier gene editing technologies involved zinc finger nucleases and transcription activator-like effector nucleases, but the third-generation gene editing technology uses clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). The rapid development of CRISPR/Cas9 technology has made it one of the most effective, straightforward, affordable, and user-friendly technologies for targeted gene editing. This review summarizes the application of CRISPR/Cas9 technology in soybean molecular breeding. More specifically, it provides an overview of the genes that have been targeted, the type of editing that occurs, the mechanism of action, and the efficiency of gene editing. Furthermore, suggestions for enhancing and accelerating the molecular breeding of novel soybean varieties with ideal traits (e.g., high yield, high quality, and durable disease resistance) are included.

Genotyping by Sequencing for SNP-Based Linkage Analysis and the Development of KASPar Markers for Male Sterility and Polyembryony in Citrus

Polyembryony and male sterility (MS) are essential characters for citrus breeding. MS, coupled with parthenocarpy, allows for addressing the diversification of diploid seedless mandarin varieties, and nucleocytoplasmic MS is the most prevalent system. Polyembryony limits the use of seed parents in scion breeding programs, and the recovery of monoembryonic hybrids to be used as female parents is a crucial pre-breeding component. The objectives of this work were the identification of SNPs closely linked with the genes implied in these traits for marker-assisted selection. Genotyping by sequencing was used to genotype 61 diploid hybrids from an F1 progeny recovered from crossing 'Kiyomi' and 'Murcott' tangors. A total of 6444 segregating markers were identified and used to establish the two parental genetic maps. They consisted of 1374 and 697 markers encompassing 1416.287 and 1339.735 cM for 'Kiyomi' and 'Murcott', respectively. Phenotyping for MS and polyembryony was performed. The genotype-trait association study identified a genomic region on LG8 which was significantly associated with MS, and a genomic region on LG1 which was significantly associated with polyembryony. Annotation of the identified region for MS revealed 19 candidate genes. One SNP KASPar marker was developed and fully validated for each trait.

Integrated transcriptomic and proteomic analysis of a cytoplasmic male sterility line and associated maintainer line in soybean

INTRODUCTION

Heterosis is a critical phenomenon in crop improvement. Cytoplasmic male sterility (CMS) and Restorer gene (Rf) systems are essential components for heterosis-based breeding. However, the molecular mechanism underlying CMS remains largely unclear in soybean.

METHODS

We integrated a morphological investigation with comparative analyses of transcriptomic and proteomic changes in pollen from the CMS line W931A and its maintainer line, W931B, at the uninucleate microspore (UM) and binucleate pollen (BP) stages.

RESULTS

Compared to W931B, which had healthy, oval pollen grains, W931A showed shrunken or degraded pollen grains with an irregularly thickened endothelium and decreased starch accumulation. Transcriptomic comparisons revealed a total of 865 differentially expressed genes (DEGs) in W931A over the two stages. These genes were primarily associated with pentose and glucuronate interconversions, sphingolipid metabolism, and glycerolipid metabolism. Proteomic analysis revealed 343 differentially expressed proteins (DEPs), which were mainly involved in carbon metabolism, glycolysis/gluconeogenesis, and nitrogen metabolism. Consistently, Gene Ontology (GO) biological process terms related to pollen development were enriched among DEGs at the UM and BP stages. Notably, four genes with demonstrated roles in pollen development were differentially expressed, including AGAMOUS-LIKE 104, PROTEIN-TYROSINE-PHOSPHATASE 1, and PHOSPHOLIPASE A2. A total of 53 genes and the corresponding proteins were differentially expressed in W931A at both the UM and BP stages, and many of these were pectinesterases, polygalacturonases, peroxidases, and ATPases.

DISCUSSION

The results of this study suggest that pollen development in W931A is likely regulated through suppression of the identified DEGs and DEPs. These findings increase our understanding of the molecular mechanism underlying CMS in soybean, aiding future research into soybean fertility and promoting the efficient use of heterosis for soybean improvement.

Harnessing heterosis and male sterility in soybean [Glycine max (L.) Merrill]: A critical revisit

Soybean is a predominantly self-pollinated crop. It is also one of the important oilseed legumes. Soybean is an excellent crop having industrial, traditional, culinary, feeding, and cultural roles. Genetic diversity in breeding programs is of prime importance as it ensures the success of any breeding by enhancing the outcomes and results of the plants. The phenomenon wherein the progeny exhibits greater biomass (yield) and a faster rate of development and fertility than its parents is referred to as heterosis. As of now, heterosis is mainly limited to the trait of seed yield and is considered the basis for the development of better (superior) varieties. Male sterility (MS) is extensively used for the production of seeds and the improvement of crops coupled with the traditional breeding programs and molecular technology. Therefore, deployment of MS and heterosis in breeding soybean could yield better outcomes. This review aims to focus on two aspects, namely, MS and heterosis in soybean with its scope for crop improvement.

TaEXPB5 functions as a gene related to pollen development in thermo-sensitive male-sterility wheat with Aegilops kotschyi cytoplasm

The thermo-sensitive cytoplasmic male-sterility line with Aegilops kotschyi cytoplasm (K-TCMS) is completely male sterile under low temperature (< 18 ℃) during Zadoks growth stages 45-52, whereas its fertility can be restored under hot temperature (≥ 20 ℃). The K-TCMS line may facilitate hybrid breeding and hybrid wheat production. Therefore, to elucidate the molecular mechanisms of its male sterility/fertility conversion, we conducted the association analysis of proteins and transcript expression to screen fertility related genes using RNA-seq, iTRAQ, and PRM-based assay. A gene encoding expansin protein in wheat, TaEXPB5, was isolated in K-TCMS line KTM3315A, which upregulated expression in the fertility anthers. Subcellular localization analysis suggested that TaEXPB5 protein localized to nucleus and cell wall. The silencing of TaEXPB5 displayed pollen abortion and the declination of fertility. Further, cytological investigation indicated that the silencing of TaEXPB5 induced the early degradation of tapetum and abnormal development of pollen wall. These results implied that TaEXPB5 may be essential for anther or pollen development and male fertility of KTM3315A. These findings provide a novel insight into molecular mechanism of fertility conversion for thermo-sensitive cytoplasmic male-sterility wheat, and contribute to the molecular breeding of hybrid wheat in the future.

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.

Integrative Analysis of Transcriptomic and Proteomic Changes Related to Cytoplasmic Male Sterility in Spring Stem Mustard (Brassica juncea var. tumida Tsen et Lee)

The development of flower and pollen is a complex biological process that involves multiple metabolic pathways in plants. In revealing novel insights into flower and pollen development underlying male sterility (MS), we conducted an integrated profiling of gene and protein activities in developing buds in cytoplasmic male sterile (CMS) mutants of mustard (Brassica juncea). Using RNA-Seq and label-free quantitative proteomics, 11,832 transcripts and 1780 protein species were identified with significant differential abundance between the male sterile line 09-05A and its maintainer line 09-05B at the tetrad stage and bi-nucleate stage of B. juncea. A large number of differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) involved in carbohydrate and energy metabolism, including starch and sucrose metabolism, tricarboxylic acid (TCA) cycle, glycolysis, and oxidoreductase activity pathways, were significantly downregulated in 09-05A buds. The low expression of these DEGs or functional loss of DAPs, which can lead to an insufficient supply of critical substrates and ATP, could be associated with flower development, pollen development, and changes in fertility in B. juncea. Therefore, this study provided transcriptomic and proteomic information of pollen abortion for B. juncea and a basis for further research on the molecular regulatory mechanism of MS in plants.

Application of iTRAQ Technology to Identify Differentially Expressed Proteins of Sauce Lamb Tripe with Different Secondary Pasteurization Treatments

Vacuum-packed sauce lamb tripe was subjected to secondary pasteurization by high-pressure processing (HPP) and heat treatment (HT), and iTRAQ technology was applied to investigate the differentially expressed proteins (DEPs). The analysis revealed 484 and 398 DEPs in the HPP and HT samples, respectively, compared with no treatment. These DEPs were sorted by texture results, and it was revealed that these DEPs acted in different biological processes with many structural proteins and protein subunits related to lamb tripe texture. The results verified by Western blot were consistent with the protein expression changes observed by proteomics. The bioinformatics analysis showed that the hardness and gumminess of the sauce lamb tripe after HT might be related to changes in the expression of CNN1 and FN1. The changes in the expression of TMP, FN1, YWHAG, TTN, collagen isoforms, and ARPC3 might be related to the improved springiness and chewiness of lamb tripe after HPP.

Proteomic analysis of body wall and coelomic fluid in Sipunculus nudus

In order to make clear the protein compositions of Sipunculus nudus and investigate its immune-related proteins, proteomic analysis was performed on body wall and coelomic fluid of Sipunculus nudus. A total of 1659 proteins were identified, and 539 proteins were differentially expressed in the coelomic fluid compared to those in the body wall, of which 415 proteins were up-regulated while 124 proteins were down-regulated. Gene Ontology (GO) analysis showed that the GO terms involved in the two parts of Sipunculus nudus were similar, with metabolic processes, catalytic activity and cell occupying the top categories of biological process, molecular function and cellular component, respectively. KEGG pathway analysis showed that 49 pathways in body wall and 48 in coelomic fluid were mapped respectively, and these pathways were mainly related to cellular processes, environmental information processing, genetic information processing and metabolism. The COG analysis showed that 757 proteins from body wall and 889 from coelomic fluid were classified into 26 COG categories, respectively. Pfam annotation revealed the mainly immune-related proteins contained in Sipunculus nudus, such as insulin-like growth factor binding protein, catalase, basement membrane proteoglycan, titin. Our research provides the first proteomic information of Sipunculus nudus, which contributes to the study of functional proteins in Sipunculus nudus and is of great significance for the application of Sipunculus nudus in functional foods and medicines.

Identification and verification of genes related to pollen development and male sterility induced by high temperature in the thermo-sensitive genic male sterile wheat line

Bioinformatic analysis identified the function of genes regulating wheat fertility. Barley stripe mosaic virus-induced gene silencing verified that the genes TaMut11 and TaSF3 are involved in pollen development and related to fertility conversion. Environment-sensitive genic male sterility is of vital importance to hybrid vigor in crop production and breeding. Therefore, it is meaningful to study the function of the genes related to pollen development and male sterility, which is still not fully understand currently. In this study, YanZhan 4110S, a new thermo-sensitive genic male sterility wheat line, and its near-isogenic line YanZhan 4110 were analyzed. Through comparative transcriptome basic bioinformatics and weighted gene co-expression network to further identify some hub genes, the genes TaMut11 and TaSF3 associated with pollen development and male sterility induced by high-temperature were identified in YanZhan 4110S. Further verification through barley stripe mosaic virus-induced gene silencing elucidated that the silencing of TaMut11 and TaSF3 caused pollen abortion, finally resulting in the declination of fertility. These findings provided data on the abortive mechanism in environment-sensitive genic male sterility wheat.

iTRAQ and PRM-based comparative proteomic profiling in gills of white shrimp Litopenaeus vannamei under copper stress

Crustaceans are particularly sensitive to heavy metal pollution. Copper (Cu) is one of typical heavy metal pollutants in aquatic ecosystems. However, limited attention has been paid on the proteomic responses of shrimp under Cu stress. White shrimp Litopenaeus vannamei held in 5‰ seawater were exposed to 5 mg L^-1 Cu for 3 h, and the regulatory mechanism in the gills was elucidated using iTRAQ-based quantitative proteomics. The results showed that a total of 5034 proteins were identified, 385 differentially expressed proteins (DEPs), including 147 differentially up-regulated proteins (DUPs) and 238 differentially down-regulated proteins (DDPs) were found. Bioinformatics analysis indicated the DEPs responding to Cu stress mainly involved in cytoskeleton, immune response, stress response, protein synthesis, detoxification, ion homeostasis and apoptosis. Furthermore, we still performed PRM analysis on sarcoplasmic calcium binding protein (SCP), serine proteinase inhibitor B3 (SPIB3), C-type lectin 4 (CTL4), cathepsin L (CATHL), JHE-like carboxylesterase 1 (CXE1) and paramyosin (PMY), and biochemical analysis on Cu/Zn-superoxide dismutase (Cu/Zn-SOD) to validate the iTRAQ results, respectively. The present proteome analysis revealed that Cu stress disrupted the ion homeostasis and protein synthesis, and L.vannamei mainly regulates a series of molecular pathways which contained many key proteins involved in the immune process to protect the organism from Cu stress. Our data provides more insight about the underlying mechanisms that related to the stress response of Cu exposure in crustacean.

Effect of temperature fluctuation on colour change and softening of postharvest sweet cherry

The inevitable temperature fluctuation during cold chain transport accelerates the colour change and softening of postharvest sweet cherry, leading to further deterioration of quality and decline of the marketable value of cherries. The influences of temperature fluctuation on the contents of total anthocyanin, phenolic, malondialdehyde, and sodium carbonate-soluble pectin (SSP), as well as the activities of polyphenoloxidase (PPO) and peroxidase (POD) in sweet cherry, were assessed. In addition, the effects of temperature fluctuation on the activities of polygalacturonase (PG), pectin methyl esterase (PME), and beta-galactosidase (β-Gal) activities, and the paPG, paPME, and paPME genes expression were studied. The evolution of SSP nano-morphology was measured by atomic force microscopy. The results showed that the temperature fluctuation promoted anthocyanin synthesis, phenolic metabolism, and malondialdehyde accumulation, which immediately affected the brightness (6.2% lower than that of the cherry stored at 5 °C) of sweet cherry. Temperature fluctuation also led to a significant increase in POD and PPO activities during subsequent isothermal storage, accelerating the colour change (24.8% more than that of the cherry stored at 5 °C), which almost reached the level observed during constant 10 °C storage. In addition, temperature fluctuation not only affected the firmness (13.7% lower than that of the cherry stored at a constant temperature of 5 °C) of fruit immediately, but also, during subsequent isothermal storage, accelerated the deterioration of firmness (19.6% lower than that of the cherry stored at a constant temperature of 5 °C). This could be explained by temperature fluctuation inducing the upregulation of paPG1-3, paPME3, and paPME4 expression, which led to a 3.5 and 1.5-fold increase in PG and PME activity, respectively. This led to degradation of the aggregated SSP to its nanostructural basic units. Furthermore, temperature fluctuation resulted in upregulated expression of paβ-Gal1 and paβ-Gal3 and enhanced β-Gal activity during subsequent isothermal storage. The results provide theoretical guidance for the transportation, storage, and preservation of postharvest sweet cherry.

The inevitable temperature fluctuation induced anthocyanin synthesis, phenolic metabolism, and alkali-soluble pectin degradation, which lead to sweet cherry enzymatic browning and softening.

Proteomics and Lipidomics Investigations to Decipher the Behavior of Willaertia magna C2c Maky According to Different Culture Modes

Willaertia magna C2c Maky is a free-living amoeba that has demonstrated its ability to inhibit the intracellular multiplication of some Legionella pneumophila strains, which are pathogenic bacteria inhabiting the aquatic environment. The Amoeba, an industry involved in the treatment of microbiological risk in the water and plant protection sectors, has developed a natural biocide based on the property of W. magna to manage the proliferation of the pathogen in cooling towers. In axenic liquid medium, amoebas are usually cultivated in adhesion on culture flask. However, we implemented a liquid culture in suspension using bioreactors in order to produce large quantities of W. magna. In order to investigate the culture condition effects on W. magna, we conducted a study based on microscopic, proteomics and lipidomics analyzes. According to the culture condition, amoeba exhibited two different phenotypes. The differential proteomics study showed that amoebas seemed to promote the lipid metabolism pathway in suspension culture, whereas we observed an upregulation of the carbohydrate pathway in adherent culture. Furthermore, we observed an over-regulation of proteins related to the cytoskeleton for W. magna cells grown in adhesion. Regarding the lipid analysis, suspension and adhesion cell growth showed comparable lipid class compositions. However, the differential lipid analysis revealed differences that confirmed cell phenotype differences observed by microscopy and predicted by proteomics. Overall, this study provides us with a better insight into the biology and molecular processes of W. magna in different culture lifestyles.

Differential proteomic analysis of soybean anthers by iTRAQ under high-temperature stress

High-temperature has severe impacts on the functionality and development of soybean male reproductive organs. However, the molecular mechanism of thermo-tolerance in soybean remains unclear. In this study, a differential proteomic analysis was conducted between the anthers of heat-tolerant (JD21) and heat-sensitive (HD14) cultivars using an iTRAQ based approach. In total, 371, 479, and 417 differentially abundant proteins were identified between HD14 anthers treated with high-temperature stress vs HD14 anthers in the natural field conditions, JD21 anthers treated with high-temperature stress vs JD21 anthers in the natural field conditions, and HD14 vs JD21 anthers treated with high-temperature stress, respectively. The differentially abundant proteins associated with thermo-tolerance were predominantly involved in carbohydrate and energy metabolism, protein synthesis and degradation, nitrogen assimilation, and ROS detoxification. Sixteen common differentially abundant proteins were involved in known protein-protein interaction networks in three comparisons associated with heat, which may strongly influence anther growth and development. The qRT-PCR analysis validated the reliability of the iTRAQ results. In conclusion, the heat-tolerant cultivar performed better under stress than heat-sensitive cultivar through modulation of HSP family proteins, pectinesterase, profilin, S-adenosylmethionine synthase, peroxidase, GST, peptidylprolyl isomerase, and disulfide-isomerase. The results provide novel insight into the mechanism of high-temperature stress response of soybean. SIGNIFICANCE: In recent years, with the high temperature (HT) stress brought by climate change frequently occurs at anthesis and negatively affects soybean productivity. The molecular mechanism underlying the response of soybean anthers to HT is a relatively complex process and thus difficult to elucidate; however, it is possible to identify differentially expressed genes or proteins between heat-sensitive and heat-tolerant cultivars under HT stress. The potential candidate genes or proteins may then be utilized in elucidating the molecular mechanism underlying the response of soybean to HT stress, as well as provide genetic resource for the improvement of heat-tolerant characteristics in soybean. In present study, quantitative and qualitative proteomic changes occurring in anthers were compared between the heat-tolerant (JD21) and heat-sensitive (HD14) cultivars under HT stress using iTRAQ-based proteomics strategy. Our results provide new insight into translational alterations in HT-resistant and HT-sensitive soybean cultivars under HT stress, which helps to address the underlying molecular mechanism of soybean in response to HT stress.

TMT-based quantitative proteomics analyses of sterile/fertile anthers from a genic male-sterile line and its maintainer in cotton (Gossypium hirsutum L.)

Genetic male sterility (GMS) in cotton is important for utilization of heterosis. However, the molecular mechanism of GMS is poorly known. In this study, cytological and proteomics analyses of anthers were conducted in three stages (stage 3 to 5) between GMS line (GA18) and its maintainer (GA18M). The cross-section observation revealed that the tapetal layer in stage 3 was thinner in GA18 compared to GA18M, and the tapetum cells did not degrade in stage 4 in GA18, thus providing no material for microspore development. A total of 1952 differentially expressed proteins (DEPs) were identified between GA18 and GA18M anthers. They were annotated to 52 gene ontology (GO) terms and enriched in 115 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which formed several complex regulator networks, and dozens of important nodes were identified. Moreover, DEPs were also identified between two consecutive stages of GA18 and GA18M, with functional analyses indicating that numerous developmental differences existed between fertile and sterile anthers. The metabolic pathways were significantly altered, including decreased carbohydrate metabolism, ribosome defects, disturbed protein synthesis, disrupted flavonoids synthesis, etc., that may be involved in male sterility. Overall, these results provide genetic resources that help decipher the molecular mechanisms behind GMS. SIGNIFICANCE: Male sterility is a common phenomenon in flowering plant species, and plays a role in the application of heterosis. However, the molecular mechanism of it remains to be elucidated. Using cytological and proteomics approaches, we found that the tapetal layer development retardation may be the reason of male sterility, which was different from the delayed degradation described in previous studies. More than one thousand differentially expressed proteins were identified between male sterile line and its maintainer, forming a complex regulatory network, and the key nodes were remarked that could be used as candidate proteins related to male sterility in future study. Dozens of metabolic pathways were significantly altered, among them, ribosome defects was a novel pathway that may be involved in male sterility. These results enhance our understanding of the molecular mechanism governing male sterility and lay a foundation for clone of genes association with male sterility.

Mitochondrial proteomic analysis reveals that proteins relate to oxidoreductase activity play a central role in pollen fertility in cotton

Cotton (Gossypium hirsutum L.) is an important economic crop. Cytoplasm male sterility (CMS) has been used to develop hybrid system and to produce hybrid seeds in cotton, but the molecular mechanism of CMS remains unclear. Mitochondria are semi-autonomous organelles, which play an important role in the reproduction of flowering plants. Male sterility has been proved associated with mitochondrial dysfunction in plants. In present study, a new strategy of proteomic sequencing data-independent acquisition (DIA) was used to analysis protein abundance across CMS lines 2074A (cytoplasm of Gossypium harknessii, D_2-2) and 2074S (cytoplasm of G. hirsutum, AD₁), and their maintainer 2074B. Comparing with transcriptome results showed that there is little consistence between proteome and transcriptome. A total of 2095 protein species were identified in three materials, and 186 and 161 differentially proteins were detected in the comparisons of 2074A vs 2074B, and 2074S vs 2074B, respectively. Among them, 49 and 50 proteins were specific existed in anther, and mainly participated in oxidoreductase activity, carbohydrate metabolism, fatty acid metabolism, cell aging, wax or cutin deposition and signal transduction. Gh_A07G0770 and Gh_D05G1908 were specific up-regulated in sterility lines, and the other genes Gh_D08G1196, Gh_D12G1971, Gh_A11G1250, Gh_D08G0388 were down-regulated, which presented similar expression tendency verified by qRT-PCR, transcriptome and proteome results. These six genes related to lipid synthesis, response to oxidative stress and cell aging, suggested them being involved in CMS occurrence. Using virus-induced gene silencing (VIGS) system, sterility obtained demonstrated the silencing Gh_A11G1250 in maintainer 2074B led to partial anthers abortion. Gh_A11G1250 encoded a mitochondrial localization of peroxisomal-like protein, participated in response to reactive oxygen species (ROS). Twenty-two proteins interacting with Gh_A11G1250 mainly related to chlorophyll biosynthetic process, photoperiodism and flowering, which showed different expression pattern between the male sterile line 2074A and maintainer 2074B. This novel research based on mitochondrial proteomics comparison confirmed that DAPs related to oxidative stress are critical to pollen abortion. BIOLOGICAL SIGNIFICANCE: Cytoplasm male sterility (CMS) system is utilized widely for hybrid production in cotton. However, the genetic and molecular mechanisms of CMS still need to be further elucidated. Up till now, fewer comprehensive comparisons of the mitochondrial proteomes from cotton CMS line and maintainer line have been reported. In this study, we performed a novel comparison of mitochondrial protein profiles in two CMS lines and their common maintainer line. Based on our results, we found a potential protein related to oxidative stress led to the anthers abortion. These results accumulate data to interpret the molecular mechanisms of CMS in cotton.

iTRAQ-Based Proteomics Reveals that the Tomato ms1035 Gene Causes Male Sterility through Compromising Fat Acid Metabolism

So far, over 50 spontaneous male sterile mutants of tomato have been described and most of them are categorized as genetic male sterility. To date, the mechanism of tomato genetic male sterility remained unclear. In this study, differential proteomic analysis is performed between genetic male sterile line (2-517), which carries the male sterility (ms10³⁵ ) gene, and its wild-type (VF-11) using isobaric tags for relative and absolute quantification-based strategy. A total of 8272 proteins are quantified in the 2-517 and VF-11 lines at the floral bud and florescence stages. These proteins are involved in different cellular and metabolic processes, which express obvious functional tendencies toward the hydroxylation of the ω-carbon in fatty acids, the tricarboxylic acid cycle, the glycolytic, and pentose phosphate pathways. Based on the results, a protein network explaining the mechanisms of tomato genetic male sterility is proposed, finding the compromising fat acid metabolism may cause the male sterility. These results are confirmed by parallel reaction monitoring, quantitative Real-time PCR (qRT-PCR), and physiological assays. Taken together, these results provide new insights into the metabolic pathway of anther abortion induced by ms10³⁵ and offer useful clues to identify the crucial proteins involved in genetic male sterility in tomato.

Comparative transcriptome analysis indicates conversion of stamens into pistil-like structures in male sterile wheat (Triticum aestivum L.) with Aegilops crassa cytoplasm

BACKGROUND

Aegilops crassa cytoplasm is an important source for investigating cytoplasmic male sterility (CMS). Moreover, the stamens of line C303A exhibit a high degree of pistillody, turning almost white. However, the molecular mechanism that underlies pistillody in C303A remains unclear. Therefore, to obtain a better understanding of pistillody in C303A, the phenotypic and cytological features of C303A were observed to identify the key stage for the homeotic transformation of stamens into pistil-like structures. Transcriptome profiles were determined for stamens using Illumina RNA sequencing.

RESULTS

Morphological observations of the CMS wheat line with Aegilops crassa cytoplasm C303A showed that the pistils developed normally, but the stamens were ultimately aborted and they released no pollen when mature. According to paraffin section observations, the stamens began to transform into pistils or pistil-like structures in the binucleate stage (BNS). Therefore, the stamens were collected from line C303A and its maintainer 303B in the BNS for transcriptome sequencing. In total, 20,444 wheat genes were determined as differentially expressed in C303A and 303B stamens, with 10,283 upregulated and 10,161 downregulated genes. Gene Ontology enrichment analyses showed that most of the differentially expressed genes (DEGs) were annotated with GO terms comprising metabolic process, cell, cellular process, catalytic activity, and cell part. Analysis based on the Kyoto Encyclopedia of Genes and Genomes database showed that the enriched DEGs were mainly associated with energy metabolism. We also found several essential genes that may contribute to pistillody in C303A. These findings suggest that disrupted energy metabolism and reactive oxygen metabolism induce pistillody and eventually lead to abortion in C303A.

CONCLUSION

We determined the complex transcriptome profiles for C303A stamens and demonstrated that disrupted energy metabolism and class B MADS-box genes are related to pistillody. These findings may facilitate future studies of the mechanistic response of the wheat stamen and pollen development in CMS.

iTRAQ-based proteomic analysis reveals several key metabolic pathways associated with male sterility in Salvia miltiorrhiza

Male sterility is a common phenomenon in flowering plants, and it has been widely used in hybrid seed production in a number of economically important crops. In 2002, our team discovered a natural male sterile mutant of Salvia miltiorrhiza. It provided us with the possibility of obtaining stable and controllable quality. To study the molecular mechanism of male sterility in S. miltiorrhiza, we generated proteomic profiles comparing the male sterile mutant type (MT) and wild type (WT) using iTRAQ sequencing. We found a total of 639 differential abundant proteins (DAPs) between MT and WT buds. The DAPs associated with male sterility were mainly involved in (1) carbohydrate and energy metabolism, and (2) protein synthesis and degradation. Based on a comparison between the protein expression profiles of MT and WT, we elucidated a potential protein interaction network involved in male sterility. These results provide new potential biomarkers and insights into the molecular mechanism of male sterility in S. miltiorrhiza.

Male sterility is a common phenomenon in flowering plants, and it has been widely used in hybrid seed production in a number of economically important crops.

Integrative Proteomic and MicroRNA Analysis: Insights Into Mechanisms of Eyestalk Ablation-Induced Ovarian Maturation in the Swimming Crab Portunus trituberculatus

Eyestalk ablation is the most common method to induce ovarian maturation in decapod crustacean aquaculture, but it jeopardizes broodstock survival and larvae production. It is important to understand the molecular basis underlying the maturation triggered by ablation and thereby develop an alternative measure for maturation manipulation. In this study, we investigate alterations of ovarian proteome and miRNA profile after ablation in a commercially important marine crab Portunus trituberculatus. Quantitative proteomic analysis using iTRAQ reveals that 163 proteins are differentially expressed following ablation, and modulation of methyl farnesoate metabolism and activation of calcium signaling may play important roles in the ovarian maturation induced by ablation. miRNA expression profiling identifies 31 miRNAs that show statistically significant changes. Integration of miRNA and proteome expression data with miRNA target prediction algorithms generates a potential regulatory network consisting of 26 miRNAs and 30 proteins linked by 71 possible functional associations. The miRNA-protein network analysis suggests that miRNAs are involved in promoting ovarian maturation by controlling expression of proteins related to methyl farnesoate synthesis, calcium signals, and energy metabolism. Experimental validation and temporal expression analysis indicate multiple miRNAs can act synergistically to regulate expression of Farnesoic acid O-methyltransferase and Calmodulin. Our findings provide new insights for elucidating the mechanisms underlying eyestalk ablation-induced ovarian maturation and could be useful for devising an alternative technique for manipulating reproduction in P. trituberculatus and other decapods.

Metabolomics Studies on Cytoplasmic Male Sterility during Flower Bud Development in Soybean

Abnormal reactive oxygen species (ROS) may mediate cytoplasmic male sterility (CMS). To observe the effect of ROS on soybean CMS, metabolite content and antioxidant enzyme activity in the flower buds between soybean N8855-derived CMS line and its maintainer were compared. Of the 612 metabolites identified, a total of 74 metabolites were significantly differentiated in flower buds between CMS line and its maintainer. The differential metabolites involved 32 differential flavonoids, 13 differential phenolamides, and 1 differential oxidized glutathione (GSSG) belonging to a non-enzymatic ROS scavenging system. We observed lower levels of flavonoids and antioxidant enzyme activities in flower buds of the CMS line than in its maintainer. Our results suggest that deficiencies of enzymatic and non-enzymatic ROS scavenging systems in soybean CMS line cannot eliminate ROS in anthers effectively, excessive accumulation of ROS triggered programmed cell death and ultimately resulted in pollen abortion of soybean CMS line.

Proteomic analysis reveals that sugar and fatty acid metabolisms play a central role in sterility of the male-sterile line 1355A of cotton

Cotton (Gossypium spp.) is one of the most important economic crops and exhibits yield-improving heterosis in specific hybrid combinations. The genic male-sterility system is the main strategy used for producing heterosis in cotton. To better understand the mechanisms of male sterility in cotton, we carried out two-dimensional electrophoresis (2-DE) and label-free quantitative proteomics analysis in the anthers of two near-isogenic lines, the male-sterile line 1355A and the male-fertile line 1355B. We identified 39 and 124 proteins that were significantly differentially expressed between these two lines in the anthers at the tetrad stage (stage 7) and uninucleate pollen stage (stage 8), respectively. Gene ontology-based analysis revealed that these differentially expressed proteins were mainly associated with pyruvate, carbohydrate, and fatty acid metabolism. Biochemical analysis revealed that in the anthers of line 1355A, glycolysis was activated, which was caused by a reduction in fructose, glucose, and other soluble sugars, and that accumulation of acetyl-CoA was increased along with a significant increase in C14:0 and C18:1 free fatty acids. However, the activities of pyruvate dehydrogenase and fatty acid biosynthesis were inhibited and fatty acid β-oxidation was activated at the translational level in 1355A. We speculate that in the 1355A anther, high rates of glucose metabolism may promote fatty acid synthesis to enable anther growth. These results provide new insights into the molecular mechanism of genic male sterility in upland cotton.

Transcriptomic and Proteomic Analysis of Shaan2A Cytoplasmic Male Sterility and Its Maintainer Line in Brassica napus

Cytoplasmic male sterility (CMS) lines are widely used for hybrid production in Brassica napus. The Shaan2A CMS system is one of the most important in China and has been used for decades; however, the male sterility mechanism underlying Shaan2A CMS remains unknown. Here, we performed transcriptomic and proteomic analysis, combined with additional morphological observation, in the Shaan2A CMS. Sporogenous cells, endothecium, middle layer, and tapetum could not be clearly distinguished in Shaan2A anthers. Furthermore, Shaan2A anther chloroplasts contained fewer starch grains than those in Shaan2B (a near-isogenic line of Shaan2A), and the lamella structure of chloroplasts in Shaan2A anther wall cells was obviously aberrant. Transcriptomic analysis revealed differentially expressed genes (DEGs) mainly related to carbon metabolism, lipid and flavonoid metabolism, and the mitochondrial electron transport/ATP synthesis pathway. Proteomic results showed that differentially expressed proteins were mainly associated with carbohydrate metabolism, energy metabolism, and genetic information processing pathways. Importantly, nine gene ontology categories associated with anther and pollen development were enriched among down-regulated DEGs at the young bud (YB) stage, including microsporogenesis, sporopollenin biosynthetic process, and tapetal layer development. Additionally, 464 down-regulated transcription factor (TF) genes were identified at the YB stage, including some related to early anther differentiation such as SPOROCYTELESS (SPL, also named NOZZLE, NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), MYB80 (formerly named MYB103), and ABORTED MICROSPORES (AMS). These results suggested that the sterility gene in the Shaan2A mitochondrion might suppress expression of these TF genes in the nucleus, affecting early anther development. Finally, we constructed an interaction network of candidate proteins based on integrative analysis. The present study provides new insights into the molecular mechanism of Shaan2A CMS in B. napus.

Cytological and iTRAQ-based quantitative proteomic analyses of hau CMS in Brassica napus L

Hau cytoplasmic male sterility (CMS) is a new type of CMS that was originally identified in Brassica juncea and subsequently transferred to B. napus and B. rapa. To further elucidate the molecular mechanism underlying hau CMS in B. napus, semithin section analysis and iTRAQ-based differential proteomic analysis were performed to compare the hau CMS and its maintainer line. Cytological analysis revealed that abnormal anther development in the hau CMS line was arrested during the differentiation of stamen archesporial cells. qRT-PCR analysis showed that the sterility gene orf288 was expressed at substantially higher levels in CMS anthers than in anthers with restored fertility. In comparison with the maintainer line, a total of 186 differentially abundant proteins were identified in the CMS line, 58 of which exhibited increased accumulation and 128 exhibited decreased accumulation. Bioinformatics analysis showed that proteins involved in carbohydrate and energy metabolism, such as those involved in oxidative phosphorylation, glycolysis/gluconeogenesis and pyruvate metabolism, exhibited decreased accumulation in the hau CMS line, whereas those involved in oxidative stress, antagonism of cell death and protein processing exhibited increased accumulation in the hau CMS line, indicating the potential roles of carbohydrate metabolism and energy supply in the regulation of hau anther abortion. BIOLOGICAL SIGNIFICANCE: Cytoplasmic male sterility (CMS) is one of the most efficient ways to produce hybrid seeds in crops. CMS is mainly caused by mitochondrial mutation and has been an important model for investigation of cytoplasmic and nuclear interactions in various plant species. Hau is a new type of CMS line in Brassica with completely abortive anthers. Although studies have been conducted to identify the key genes associated with CMS, the molecular mechanisms underlying hau CMS remain unclear. In this study, cytological, molecular, and proteomic approaches were used to reveal the mechanism underlying hau CMS in B. napus. Based on a comparison of the protein expression profiles of the hau CMS line and its maintainer line to elucidate the mechanisms underlying hau CMS, a potential protein regulatory network is proposed herein. These results may provide new insights into the molecular basis of hau CMS in B. napus.

Integrated analysis of transcriptomic and proteomic data from tree peony (P. ostii) seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism

Tree peony (Paeonia section Moutan DC.) seeds are an excellent source of beneficial natural compounds that promote health, and they contain high levels of alpha-linolenic acid (ALA). In recent years, tree peony has been emerging as an oil crop. Therefore, combined analysis of the transcriptome and proteome of tree peony (P. ostii) seeds at 25, 32, 39, 53, 67, 81, 88, 95, and 109 days after pollination (DAP) was conducted to better understand the transcriptional and translational regulation of seed development and oil biosynthesis. A total of 38,482 unigenes and 2841 proteins were identified. A total of 26,912 differentially expressed genes (DEGs) and 592 differentially expressed proteins (DEPs) were clustered into three groups corresponding to the rapid growth, seed inclusion enrichment and conversion, and late dehydration and mature stages of seed development. Fifteen lipid metabolism pathways were identified at both the transcriptome and proteome levels. Pathway enrichment analysis revealed that a period of rapid fatty acid biosynthesis occurred at 53-88 DAP. Furthermore, 211 genes and 35 proteins associated with the fatty acid metabolism pathway, 63 genes and 11 proteins associated with the biosynthesis of unsaturated fatty acids (UFAs), and 115 genes and 24 proteins associated with ALA metabolism were identified. Phylogenetic analysis revealed that 16 putative fatty acid desaturase (FAD)-encoding genes clustered into four FAD groups, eight of which exhibited the highest expression at 53 DAP, suggesting that they play an important role in ALA accumulation. RT-qPCR analysis indicated that the temporal expression patterns of oil biosynthesis genes were largely similar to the RNA-seq results. The expression patterns of fatty acid metabolism- and seed development-related proteins determined by MRM were also highly consistent with the results obtained in the proteomic analysis. Correlation analysis indicated significant differences in the number and abundance of DEGs and DEPs but a high level of consistency in expression patterns and metabolic pathways. The results of the present study represent the first combined transcriptomic and proteomic analysis of tree peony seeds and provide insight into tree peony seed development and oil accumulation.

The initial deficiency of protein processing and flavonoids biosynthesis were the main mechanisms for the male sterility induced by SX-1 in Brassica napus

Background

Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of the key genes and pathways that involved in CIMS were important to understand the underlying molecular mechanism. In the present report, a multi-omics integrative analysis, including of the proteomic, transcriptomic and miRNAs, combined with morphological and physiological analysis were conducted.

Results

Earlier degeneration of the tapetosomes and elaioplasts, aberrantly stacking in tapetal cells and incompletely deposition in tryphine of pollen wall were observed in chemical hybridization agent (CHA) of SX-1 treated B. napus through SEM and TEM analysis. It was revealed that the deficiencies in protein processing in endoplasmic reticulum (ER) and flavonoids biosynthesis were occurred at early stage in the SX-1 treated materials. Subsequently, plant hormone signal transduction, biosynthesis of amino acids, fatty acids and steroid in anther at later stages were identified down-regulated after SX-1 treatment. 144 transcript factors (TFs) were also indentified to down-regulated at early stage, which suggested the early regulation in anther and pollen wall development were disordered in CHA treated B. napus. In addition, 7 important miRNAs were identified and 2 of the predicted target genes of miRNAs were Rf-like genes.

Conclusions

Taken together, an interaction network of candidate genes and the putative metabolism pathways were constructed based on the multi-omics integrative analysis, it provided a new insight into the male sterility induced by CHA of SX-1 in B. napus.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5203-y) contains supplementary material, which is available to authorized users.

iTRAQ-Based Proteomic Analysis of Ogura-CMS Cabbage and Its Maintainer Line

Ogura cytoplasmic male sterility (CMS) contributes considerably to hybrid seed production in Brassica crops. To detect the key protein species and pathways involved in Ogura-CMS, we analysed the proteome of the cabbage Ogura-CMS line CMS01-20 and its corresponding maintainer line F01-20 using the isobaric tags for the relative and absolute quantitation (iTRAQ) approach. In total, 162 differential abundance protein species (DAPs) were identified between the two lines, of which 92 were down-accumulated and 70 were up-accumulated in CMS01-20. For energy metabolism in the mitochondrion, eight DAPs involved in oxidative phosphorylation were down-accumulated in CMS01-20, whereas in the tricarboxylic acid (TCA) cycle, five DAPs were up-accumulated, which may compensate for the decreased respiration capacity and may be associated with the elevated O2 consumption rate in Ogura-CMS plants. Other key protein species and pathways involved in pollen wall assembly and programmed cell death (PCD) were also identified as being male-sterility related. Transcriptome profiling revealed 3247 differentially expressed genes between the CMS line and the fertile line. In a conjoint analysis of the proteome and transcriptome data, 30 and 9 protein species/genes showed the same and opposite accumulation patterns, respectively. Nine noteworthy genes involved in sporopollenin synthesis, callose wall degeneration, and oxidative phosphorylation were presumably associated with the processes leading to male sterility, and their expression levels were validated by qRT-PCR analysis. This study will improve our understanding of the protein species involved in pollen development and the molecular mechanisms underlying Ogura-CMS.

Cellular and molecular characteristics of pollen abortion in chrysanthemum cv. Kingfisher

Microspore degeneration at the tetrad stage is associated with tapetum degeneration retardation. Some genes and proteins related to cell senescence and death are the key factors for pollen abortion. Chrysanthemum (Chrysanthemum morifolium) is a major floriculture crop in the world, but pollen contamination is an urgent problem to be solved in chrysanthemum production. C. morifolium 'Kingfisher' is a chrysanthemum cultivar that does not contain any pollen in mature anthers, thus it is a very important material for developing chrysanthemum without pollen contamination. However, the mechanism of its pollen abortion remains unclear. In this study, the cellular and molecular mechanisms of 'Kingfisher' pollen abortion were investigated using transmission electron microscopy, RNA sequencing, isobaric tags for relative and absolute quantitation, and bioinformatics. It was found that the meiosis of microspore mother cells was normal before the tetrad stage, the microspores began to degenerate at the tetrad stage, and no microspores were observed in the anthers after the tetrad stage. In addition, transcriptomic and proteomic analyses showed that some genes and proteins related to cell senescence and death were identified to be implicated in chrysanthemum pollen abortion. These results indicated that the tetrad stage was the main period of pollen abortion, and the genes and proteins related to cell senescence and death contributed to pollen abortion. These add to our understanding of chrysanthemum pollen abortion and will be helpful for development of flowers without pollen contamination in the future.

Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing

BACKGROUND

Cytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic genes and nuclear genes. CMS is a simple and effective pollination control system, and plays an important role in crop heterosis utilization. Circular RNAs (circRNAs) are a vital type of non-coding RNAs, which play crucial roles in microRNAs (miRNAs) function and post-transcription control. To explore the expression profile and possible functions of circRNAs in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput deep sequencing coupled with RNase R enrichment strategy was conducted.

RESULTS

CircRNA libraries were constructed from flower buds of NJCMS1A and its maintainer NJCMS1B with three biological replicates. A total of 2867 circRNAs were identified, with 1009 circRNAs differentially expressed between NJCMS1A and NJCMS1B based on analysis of high-throughput sequencing. Of the 12 randomly selected circRNAs with different expression levels, 10 showed consistent expression patterns based on high-throughput sequencing and quantitative real-time PCR analyses. Tissue specific expression patterns were also verified with two circRNAs by quantitative real-time PCR. Most parental genes of differentially expressed circRNAs were mainly involved in biological processes such as metabolic process, biological regulation, and reproductive process. Moreover, 83 miRNAs were predicted from the differentially expressed circRNAs, some of which were strongly related to pollen development and male fertility; The functions of miRNA targets were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and the target mRNAs were significantly enriched in signal transduction and programmed cell death. Furthermore, a total of 165 soybean circRNAs were predicted to contain at least one internal ribosome entry site (IRES) element and an open reading frame, indicating their potential to encode polypeptides or proteins.

CONCLUSIONS

Our study indicated that the circRNAs might participate in the regulation of flower and pollen development, which could provide a new insight into the molecular mechanisms of CMS in soybean.

Comparative proteomic analysis of Methanothermobacter thermautotrophicus reveals methane formation from H2 and CO2 under different temperature conditions

The growth of all methanogens is limited to a specific temperature range. However, Methanothermobacter thermautotrophicus can be found in a variety of natural and artificial environments, the temperatures of which sometimes even exceed the temperature growth ranges of thermophiles. As a result, the extent to which methane production and survival are affected by temperature remains unclear. To investigate the mechanisms of methanogenesis that Archaea have evolved to cope with drastic temperature shifts, the responses of Methanothermobacter thermautotrophicus to temperature were investigated under a high temperature growth (71°C) and cold shock (4°C) using Isobaric tags for relative and absolute quantitation (iTRAQ). The results showed that methane formation is decreased and that protein folding and degradation are increased in both high‐ and low‐temperature treatments. In addition, proteins predicted to be involved in processing environmental information processing and in cell membrane/wall/envelope biogenesis may play key roles in affecting methane formation and enhancing the response of M. thermautotrophicus to temperature stress. Analysis of the genomic locations of the genes corresponding to these temperature‐dependent proteins predicted that 77 of the genes likely to form 32 gene clusters. Here, we assess the response of M. thermautotrophicus to different temperatures and provide a new level of understanding of methane formation and cellular putative adaptive responses.

On the Promising Role of Enzyme Activity Assay in Interpreting Comparative Proteomic Data in Plants

Comparative proteomics is widely used to detect protein changes, especially differential abundance proteins (DAPs) that are involved in plant responses to development, disease, or environment. Once DAPs are identified, it is essential to validate any change in their abundance, and their role in the biological process under study. In addition to common confirmation by quantitative RT-PCR, immunoblot, and multiple reaction monitoring analysis, it has been proposed that enzyme activity assay (EAA) can be complementary to the standard proteomics results, especially regarding the elucidation of protein (enzyme) function and the mechanism of enzyme-associated biochemical or metabolic pathways. The enzymes discussed here are the DAPs identified in comparative plant proteomics. Despite the small number of enzymes in a proteome, they often make up a substantial proportion of the DAPs identified in comparative studies. Currently, only a few studies have performed EAA to complement the interpretation of proteomic data, especially activity-based protein profiling. This viewpoint aims to arouse the attention of proteomic researchers on the promising role of EAA in plant proteomics and highlights the need for high-throughput assays of enzyme activities in comparative plant proteomics.

Integrated analysis of transcriptome and proteome changes related to the Ogura cytoplasmic male sterility in cabbage

Cabbage (Brassica oleracea L. var. capitata), an important vegetable crop in the Brassicaceae family, is economically important worldwide. In the process of hybrid seed production, Ogura cytoplasmic male sterility (OguCMS), controlled by the mitochondrial gene orf138, has been extensively used for cabbage hybrid production with complete and stable male sterility. To identify the critical genes and pathways involved in the sterility and to better understand the underlying molecular mechanisms, the anther of OguCMS line R2P2CMS and the fertile line R2P2 were used for RNA-seq and iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) proteome analysis. RNA-seq analysis generated 13,037,109 to 13,066,594 SE50-clean reads, from the sterile and fertile lines, which were assembled into 36,890 unigenes. Among them, 1,323 differentially expressed genes (DEGs) were identified, consisting of 307 up- and 1016 down-regulated genes. For ITRAQ analysis, a total of 7,147 unique proteins were identified, and 833 were differentially expressed including 538 up- and 295 down-regulated proteins. These were mainly annotated to the ribosome, spliceosome and mRNA surveillance pathways. Combined transcriptomic and proteomic analyses identified 22 and 70 genes with the same and opposite expression profiles, respectively. Using KEGG analysis of DEGs, gibberellin mediated signaling pathways regulating tapetum programmed cell death and four different pathways involved in sporopollenin synthesis were identified. Secretion and translocation of the sporopollenin precursors were identified, and the key genes participating in these pathways were all significantly down-regulated in R2P2CMS. Light and transmission electron (TE) microscopy revealed fat abnormal tapetum rather than vacuolization and degradation at the tetrad and microspore stages of the OguCMS line. This resulted in the failed deposition of sporopollenin on the pollen resulting in sterility. This study provides a comprehensive understanding of the mechanism underlying OguCMS in cabbage.

Subcellular Proteomics: Application to Elucidation of Flooding-Response Mechanisms in Soybean

Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and during stress. Under flooding, proteins related to signaling, stress and the antioxidative system are increased in the plasma membrane; scavenging enzymes for reactive-oxygen species are suppressed in the cell wall; protein translation is suppressed through inhibition of proteins related to preribosome biogenesis and mRNA processing in the nucleus; levels of proteins involved in the electron transport chain are reduced in the mitochondrion; and levels of proteins related to protein folding are decreased in the endoplasmic reticulum. This review discusses the advantages of a gel-free/label-free proteomic technique and methods of plant subcellular purification. It also summarizes cellular events in soybean under flooding and discusses future prospects for generation of flooding-tolerant soybean.

Identification of Proteins Involved in Carbohydrate Metabolism and Energy Metabolism Pathways and Their Regulation of Cytoplasmic Male Sterility in Wheat

Cytoplasmic male sterility (CMS) where no functional pollen is produced has important roles in wheat breeding. The anther is a unique organ for male gametogenesis and its abnormal development can cause male sterility. However, the mechanisms and regulatory networks related to plant male sterility are poorly understood. In this study, we conducted comparative analyses using isobaric tags for relative and absolute quantification (iTRAQ) of the pollen proteins in a CMS line and its wheat maintainer. Differentially abundant proteins (DAPs) were analyzed based on Gene Ontology classifications, metabolic pathways and transcriptional regulation networks using Blast2GO. We identified 5570 proteins based on 23,277 peptides, which matched with 73,688 spectra, including proteins in key pathways such as glyceraldehyde-3-phosphate dehydrogenase, pyruvate kinase and 6-phosphofructokinase 1 in the glycolysis pathway, isocitrate dehydrogenase and citrate synthase in the tricarboxylic acid cycle and nicotinamide adenine dinucleotide (NADH)-dehydrogenase and adenosine-triphosphate (ATP) synthases in the oxidative phosphorylation pathway. These proteins may comprise a network that regulates male sterility in wheat. Quantitative real time polymerase chain reaction (qRT-PCR) analysis, ATP assays and total sugar assays validated the iTRAQ results. These DAPs could be associated with abnormal pollen grain formation and male sterility. Our findings provide insights into the molecular mechanism related to male sterility in wheat.

Proteomics reveals key proteins participating in growth difference between fall dormant and non-dormant alfalfa in terminal buds

To explore the molecular mechanism of growth differences between fall dormant (FD) and non-FD alfalfa, we conducted iTRAQ-based quantitative proteomics on terminal buds of Maverick (FD) and Cuf101 (non-FD) cultivars, identified differential abundance protein species (DAPS) and verified expression profiling of certain corresponding mRNA by qRT-PCR. A total of 3872 protein species were annotated. Of the 90 DAPS, 56 and 34 were respectively up- and down-accumulated in Maverick, compared to Cuf101. They were grouped into 35 functional categories and enriched in seven pathways. Of which, auxin polar transport was up-regulated, while phenylpropanoid biosynthesis, pyruvate metabolism and transportation, vitamin B1 synthesis process and flavonoid biosynthesis were down-regulated in Maverick, comparing with Cuf101. In Maverick, mRNA abundances of l-asparaginase, chalcone and stilbene synthase family protein, cinnamyl alcohol dehydrogenase-like protein, thiazole biosynthetic enzyme, pyruvate dehydrogenase E1 beta subunit, and aldo/keto reductase family oxidoreductase were significantly lower at FD than at other stages, and lower than in Cuf101. We also observed opposite mRNA profiles of thiazole biosynthetic enzyme, chalcone and stilbene synthase family protein, pyruvate dehydrogenase E1 beta subunit in both cultivars from summer to autumn. Our results suggest that these DAPS could play important roles in growth difference between FD and non-FD alfalfa.

BIOLOGICAL SIGNIFICANCE

Up to now, as far as we know, currently the proteins related with the growth differences between FD and non-FD alfalfa cultivars in autumn have not yet been identified in terminal buds. This study identified the protein species expressed in alfalfa terminal buds, selected differentially abundant protein species in terminal buds between Maverick (FD) and Cuf101 (non-FD) cultivars in autumn and identified the important protein species participated in the growth differences. This study lays a foundation for further investigation of the molecular mechanism of the growth differences between FD and non-FD alfalfa and the cultivation of advanced alfalfa cultivars.

ITRAQ-based quantitative proteomic analysis of Cynops orientalis limb regeneration

Background

Salamanders regenerate their limbs after amputation. However, the molecular mechanism of this unique regeneration remains unclear. In this study, isobaric tags for relative and absolute quantification (iTRAQ) coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) was employed to quantitatively identify differentially expressed proteins in regenerating limbs 3, 7, 14, 30 and 42 days post amputation (dpa).

Results

Of 2636 proteins detected in total, 253 proteins were differentially expressed during different regeneration stages. Among these proteins, Asporin, Cadherin-13, Keratin, Collagen alpha-1(XI) and Titin were down-regulated. CAPG, Coronin-1A, AnnexinA1, Cathepsin B were up-regulated compared with the control. The identified proteins were further analyzed to obtain information about their expression patterns and functions in limb regeneration. Functional analysis indicated that the differentially expressed proteins were associated with wound healing, immune response, cellular process, metabolism and binding.

Conclusions

This work indicated that significant proteome alternations occurred during salamander limb regeneration. The results may provide fundamental knowledge to understand the mechanism of limb regeneration.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4125-4) contains supplementary material, which is available to authorized users.

Proteomic analysis of phytase transgenic and non-transgenic maize seeds

Proteomics has become a powerful technique for investigating unintended effects in genetically modified crops. In this study, we performed a comparative proteomics of the seeds of phytase-transgenic (PT) and non-transgenic (NT) maize using 2-DE and iTRAQ techniques. A total of 148 differentially expressed proteins (DEPs), including 106 down-regulated and 42 up-regulated proteins in PT, were identified. Of these proteins, 32 were identified through 2-DE and 116 were generated by iTRAQ. It is noteworthy that only three proteins could be detected via both iTRAQ and 2-DE, and most of the identified DEPs were not newly produced proteins but proteins with altered abundance. These results indicated that many DEPs could be detected in the proteome of PT maize seeds and the corresponding wild type after overexpression of the target gene, but the changes in these proteins were not substantial. Functional classification revealed many DEPs involved in posttranscriptional modifications and some ribosomal proteins and heat-shock proteins that may generate adaptive effects in response to the insertion of exogenous genes. Protein-protein interaction analysis demonstrated that the detected interacting proteins were mainly ribosomal proteins and heat-shock proteins. Our data provided new information on such unintended effects through a proteomic analysis of maize seeds.

Genome-wide comparative analysis of DNA methylation between soybean cytoplasmic male-sterile line NJCMS5A and its maintainer NJCMS5B

BACKGROUND

DNA methylation is an important epigenetic modification. It can regulate the expression of many key genes without changing the primary structure of the genomic DNA, and plays a vital role in the growth and development of the organism. The genome-wide DNA methylation profile of the cytoplasmic male sterile (CMS) line in soybean has not been reported so far.

RESULTS

In this study, genome-wide comparative analysis of DNA methylation between soybean CMS line NJCMS5A and its maintainer NJCMS5B was conducted by whole-genome bisulfite sequencing. The results showed 3527 differentially methylated regions (DMRs) and 485 differentially methylated genes (DMGs), including 353 high-credible methylated genes, 56 methylated genes coding unknown protein and 76 novel methylated genes with no known function were identified. Among them, 25 DMRs were further validated that the genome-wide DNA methylation data were reliable through bisulfite treatment, and 9 DMRs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. Finally, 8 key DMGs possibly associated with soybean CMS were identified.

CONCLUSIONS

Genome-wide DNA methylation profile of the soybean CMS line NJCMS5A and its maintainer NJCMS5B was obtained for the first time. Several specific DMGs which participated in pollen and flower development were further identified to be probably associated with soybean CMS. This study will contribute to further understanding of the molecular mechanism behind soybean CMS.

Proteomic analysis of peel browning of 'Nanguo' pears after low-temperature storage

BACKGROUND

Postharvest ripening of the 'Nanguo' pear (Pyrus ussuriensis Maxim.) can be impeded by low-temperature storage. However, pears after long-term refrigeration are prone to peel browning when returned to room temperature conditions. This study investigated the browning mechanism of 'Nanguo' pear stored at a low temperature by analysing the differentially expressed proteins between healthy fruit and fruit with peel browning.

RESULTS

The results showed that 181 proteins underwent statistically significant changes. A categorisation of the disparately accumulated proteins was performed using gene ontology annotation. The results showed that the 'metabolic process', 'cellular process', 'catalytic activity', and 'binding' proteins were the most affected after low-temperature storage. Further analysis revealed that the differentially expressed proteins, which are related to peel browning, are primarily involved in the phenylpropanoid pathway, linoleic acid pathways, fatty acid biosynthesis pathway, glutathione metabolism pathway, photosynthesis pathway, oxidative phosphorylation pathway, and glycolysis pathway.

CONCLUSION

This study reveals that there are variations in key proteins in 'Nanguo' pear after low-temperature storage, and the identification of these proteins will be valuable in future functional genomics studies, as well as provide protein resources that can be used in the efforts to improve pear quality. © 2016 Society of Chemical Industry.

Profiling of Host Cell Response to Successive Canine Parvovirus Infection Based on Kinetic Proteomic Change Identification

Canine parvovirus (CPV) reproduces by co-opting the resources of host cells, inevitably causing cytotoxic effects to the host cells. Feline kidney F81 cells are sensitive to CPV infection and show disparate growing statuses at different time points post-infection. This study analysed the response of F81 cells to CPV infection at successive infection time points by iTRAQ-based quantitative proteomics. Differentially expressed proteins (DEPs) during 60 h of infection and at selected time points post-infection were identified by an analysis of variance test and a two-tailed unpaired t test, respectively. DEPs with similar quantitative changes were clustered by hierarchical clustering and analysed by gene ontology enrichment, revealing that 12 h and 60 h post-infection were the optimal times to analyse the autonomous parvovirus replication and apoptosis processes, respectively. Using the Metacore^TM database, 29 DEPs were enriched in a network involved in p53 regulation. Besides, a significantly enriched pathway suggests that the CPV-induced cytopathic effect was probably due to the deficiency of functional CFTR caused by CPV infection. This study uncovered the systemic changes in key cellular factors involved in CPV infection and help to understand the molecular mechanisms of the anti-cancer activity of CPV and the cytopathic effects induced by CPV infection.