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

Industrial chicory genome gives insights into the molecular timetable of anther development and male sterility

Industrial chicory (Cichorium intybus var. sativum) is a biannual crop mostly cultivated for extraction of inulin, a fructose polymer used as a dietary fiber. F1 hybrid breeding is a promising breeding strategy in chicory but relies on stable male sterile lines to prevent self-pollination. Here, we report the assembly and annotation of a new industrial chicory reference genome. Additionally, we performed RNA-Seq on subsequent stages of flower bud development of a fertile line and two cytoplasmic male sterile (CMS) clones. Comparison of fertile and CMS flower bud transcriptomes combined with morphological microscopic analysis of anthers, provided a molecular understanding of anther development and identified key genes in a range of underlying processes, including tapetum development, sink establishment, pollen wall development and anther dehiscence. We also described the role of phytohormones in the regulation of these processes under normal fertile flower bud development. In parallel, we evaluated which processes are disturbed in CMS clones and could contribute to the male sterile phenotype. Taken together, this study provides a state-of-the-art industrial chicory reference genome, an annotated and curated candidate gene set related to anther development and male sterility as well as a detailed molecular timetable of flower bud development in fertile and CMS lines.

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.

Cytosolic disproportionating enzyme2 is essential for pollen germination and pollen tube elongation in rice

Degradation of starch accumulated in pollen provides energy and cellular materials for pollen germination and pollen tube elongation. Little is known about the function of cytosolic disproportionating enzyme2 (DPE2) in rice (Oryza sativa). Here, we obtained several DPE2 knockout mutant (dpe2) lines via genomic editing and found that the mutants grew and developed normally but with greatly reduced seed-setting rates. Reciprocal crosses between dpe2 and wild-type plants demonstrated that the mutant was male sterile. In vitro and in vivo examinations revealed that the pollen of the dpe2 mutant developed and matured normally but was defective in germination and elongation. DPE2 deficiency increased maltose content in pollen, whereas it reduced the levels of starch, glucose, fructose, and adenosine triphosphate (ATP). Exogenous supply of glucose or ATP to the germination medium partially rescued the pollen germination defects of dpe2. The expression of cytosolic phosphorylase2 (Pho2) increased significantly in dpe2 pollen. Knockout of Pho2 resulted in a semi-sterile phenotype. We failed to obtain homozygous dpe2 pho2 double mutant lines. Our results demonstrate that maltose catalyzed by DPE2 to glucose is the main energy source for pollen germination and pollen tube elongation, while Pho2 might partially compensate for deficiency of DPE2.

Homology-based identification of candidate genes for male sterility editing in upland cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) accounts for more than 90% of the world's cotton production, providing natural material for the textile and oilseed industries worldwide. One strategy for improving upland cotton yields is through increased adoption of hybrids; however, emasculation of cotton flowers is incredibly time-consuming and genetic sources of cotton male sterility are limited. Here we review the known biochemical modes of plant nuclear male sterility (NMS), often known as plant genetic male sterility (GMS), and characterized them into four groups: transcriptional regulation, splicing, fatty acid transport and processing, and sugar transport and processing. We have explored protein sequence homology from 30 GMS genes of three monocots (maize, rice, and wheat) and three dicots (Arabidopsis, soybean, and tomato). We have analyzed evolutionary relationships between monocot and dicot GMS genes to describe the relative similarity and relatedness of these genes identified. Five were lowly conserved to their source species, four unique to monocots, five unique to dicots, 14 highly conserved among all species, and two in the other category. Using this source, we have identified 23 potential candidate genes within the upland cotton genome for the development of new male sterile germplasm to be used in hybrid cotton breeding. Combining homology-based studies with genome editing may allow for the discovery and validation of GMS genes that previously had no diversity observed in cotton and may allow for development of a desirable male sterile mutant to be used in hybrid cotton production.

Comparative Transcriptome Analysis Reveals Key Insights into Fertility Conversion in the Thermo-Sensitive Cytoplasmic Male Sterile Wheat

Thermo-sensitive cytoplasmic male sterility (TCMS) plays a crucial role in hybrid production and hybrid breeding; however, there are few studies on molecular mechanisms related to anther abortion in the wheat TCMS line. In this study, FA99, a new wheat thermo-sensitive cytoplasmic male sterility line, was investigated. Fertility conversion analysis showed that FA99 was mainly controlled by temperature, and the temperature-sensitive stage was pollen mother cell formation to a uninucleate stage. Further phenotypic identification and paraffin section showed that FA99 was characterized by indehiscent anthers and aborted pollen in a sterile environment and tapetum was degraded prematurely during the tetrad period, which was the critical abortion period of FA99. The contents of O^2-, H₂O₂, MDA and POD were significantly changed in FA99 under a sterile environment by the determination of physiological indexes. Furthermore, through transcriptome analysis, 252 differentially expressed genes were identified, including 218 downregulated and 34 upregulated genes. Based on KOG function classification, GO enrichment and KEGG pathways analysis, it was evident that significant transcriptomic changes in FA99 under different fertility environments, and the major differences were "phenylalanine metabolism", "phenylpropanoid biosynthesis", "cutin, suberine and wax biosynthesis", "phenylalanine, tyrosine and tryptophan biosynthesis" and "citrate cycle (TCA cycle)". Finally, we proposed an intriguing transcriptome-mediated pollen abortion and male sterility network for FA99. These findings provided data on the molecular mechanism of fertility conversion in thermo-sensitive cytoplasmic male sterility wheat.

The transcription factor TaGAMYB modulates tapetum and pollen development of TGMS wheat YanZhan 4110S via the gibberellin signaling

Male reproductive development in higher plants experienced a series of complex biological processes, which can be regulated by Gibberellins (GA). The transcriptional factor GAMYB is a crucial component of GA signaling in anther development. However, the mechanism of GAMYB in wheat male reproduction is less understood. Here, we found that the thermo-sensitive genic male sterilitywheat line YanZhan 4110S displayed delayed tapetum programmed cell death and pollen abortive under the hot temperature stress. Combined with RNA-Sequencing data analysis, TaGAMYB associated with fertility conversion was isolated, which was located in the nucleus and highly expressed in fertility anthers. The silencing of TaGAMYB in wheat displayed fertility decline, defects in tapetum, pollen and exine formation, where the abortion characteristics were the same as YanZhan 4110S. In addition, either hot temperature or GA3 treatment in YanZhan 4110S caused the downregulation of TaGAMYB at binucleate stage and trinucleate stage, as well as fertility decrease. Further, the transcription factor TaWRKY2 significantly changed under GA3-treatment and directly interacted with the TaGAMYB promoter by W-box cis-element. Therefore, we suggested that TaGAMYB may be essential for anther development and male fertility, and GA3 activates TaGAMYB by TaWRKY2 to regulate fertility in wheat.

Coastal Wild Grapevine Accession (Vitis vinifera L. ssp. sylvestris) Shows Distinct Late and Early Transcriptome Changes under Salt Stress in Comparison to Commercial Rootstock Richter 110

Increase in soil salinity, driven by climate change, is a widespread constrain for viticulture across several regions, including the Mediterranean basin. The implementation of salt-tolerant varieties is sought after to reduce the negative impact of salinity in grape production. An accession of wild grapevine (Vitis vinifera L. ssp. sylvestris), named AS1B, found on the coastline of Asturias (Spain), could be of interest toward the achievement of salt-tolerant varieties, as it demonstrated the ability to survive and grow under high levels of salinity. In the present study, AS1B is compared against widely cultivated commercial rootstock Richter 110, regarding their survival capabilities, and transcriptomic profiles analysis allowed us to identify the genes by employing RNA-seq and gene ontology analyses under increasing salinity and validate (via RT-qPCR) seven salinity-stress-induced genes. The results suggest contrasting transcriptomic responses between AS1B and Richter 110. AS1B is more responsive to a milder increase in salinity and builds up specific mechanisms of tolerance over a sustained salt stress, while Richter 110 maintains a constitutive expression until high and prolonged saline inputs, when it mainly shows responses to osmotic stress. The genetic basis of AS1B's strategy to confront salinity could be valuable in cultivar breeding programs, to expand the current range of salt-tolerant rootstocks, aiming to improve the adaptation of viticulture against climate change.

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.

Comparative analysis of mitochondrial genomes provides insights into the mechanisms underlying an S-type cytoplasmic male sterility (CMS) system in wheat (Triticum aestivum L.)

Cytoplasmic male sterility (CMS) has been widely used in crop cross breeding. There has been much research on wheat CMS. However, the correlation between S-type CMS and mitochondrial genome remains elusive. Herein, we sequenced the mitochondrial genome of wheat CMS line and compared it with the maintainer line. The results showed that the mitochondrial genome of CMS line encoded 26 tRNAs, 8 rRNAs, and 35 protein-coding genes, and the cob encoding complex III in which the protein coding gene is mutated. This protein is known to affect reactive oxygen (ROS) production. The analysis of ROS metabolism in developing anthers showed that the deficiency of antioxidants and antioxidant enzymes in the sterile system aggravated membrane lipid oxidation, resulting in ROS accumulation, and influencing the anther development. Herein, cob is considered as a candidate causative gene sequence for CMS.

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.

High glutamine suppresses osteogenesis through mTORC1-mediated inhibition of the mTORC2/AKT-473/RUNX2 axis

Activation of the key nutrient cellular sensors mTORC1 and mTORC2 directs the fate of mesenchymal stromal cells (MSCs). Here, we report that glutamine regulates crosstalk between mTOR complexes and lineage commitment of MSCs independent of glucose concentration. High glutamine-induced mTORC1 hyperactivation resulted in the suppression of mTORC2, which otherwise stabilizes RUNX2 via GSK3β inhibition through pAKT-473. Activation of GSK3β resulted in the ubiquitination of RUNX2, a key transcription factor for the osteogenic commitment of MSCs. However, low glutamine conditions inhibit mTORC1 hyperactivation followed by increased mTORC2 activation and RUNX2 stabilization. Under diabetic/high-glucose conditions, glutamine-triggered hyperactivation of mTORC1 resulted in mTORC2 suppression, and active GSK3β led to suppression of RUNX2. Activation of p-AMPK by metformin inhibits high glutamine-induced mTORC1 hyperactivation and rescues RUNX2 through the mTORC2/AKT-473 axis. Collectively, our study indicates the role of glutamine in modulating MSC fate through cross-talk between mTOR complexes by identifying a critical switch in signaling. It also shows the importance of glutamine in modulating molecular cues (mTORC1/p-70S6K/mTORC2/RUNX2) that are involved in driving diabetes-induced bone adipogenesis and other secondary complications.

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.

Proteomic analysis of differential anther development from sterile/fertile lines in Capsicum annuum L

Background

Pepper (Capsicum annuum L.) is a major cash crop throughout the world. Male sterility is an important characteristic in crop species that leads to a failure to produce functional pollen, and it has crucial roles in agricultural breeding and the utilization of heterosis.

Objectives

In this study, we identified many crucial factors and important components in metabolic pathways in anther and pollen development, and elucidated the molecular mechanism related to pollen abortion in pepper.

Methods

Pepper pollen was observed at different stages to detect the characteristics associated with male sterility and fertility. The phytohormone and oxidoreductase activities were detected in spectrophotometric and redox reaction assays, respectively. Proteins were extracted from male sterile and fertile pepper lines, and identified by TMT/iTRAQ (tandem mass tags/isobaric tags for relative and absolute quantitation) and LC-MS/MS (liquid chromatograph-mass spectrometer) analysis. Differentially abundant proteins (DAPs) were analyzed based on Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes database according to |fold change)| > 1.3 and P value < 0.05. DAPs were quantified in the meiosis, tetrad, and binucleate stages by parallel reaction monitoring (PRM).

Results

In this study, we screened and identified one male sterile pepper line with abnormal cytological characteristics in terms of pollen development. The peroxidase and catalase enzyme activities were significantly reduced and increased, respectively, in the male sterile line compared with the male fertile line. Phytohormone analysis demonstrated that the gibberellin, jasmonic acid, and auxin contents changed by different extents in the male sterile pepper line. Proteome analysis screened 1,645 DAPs in six clusters, which were mainly associated with the chloroplast and cytoplasm based on their similar expression levels. According to proteome analysis, 45 DAPs were quantitatively identified in the meiosis, tetrad, and binucleate stages by PRM, which were related to monoterpenoid biosynthesis, and starch and sucrose metabolism pathways.

Conclusions

We screened 1,645 DAPs by proteomic analysis and 45 DAPs were related to anther and pollen development in a male sterile pepper line. In addition, the activities of peroxidase and catalase as well as the abundances of phytohormones such as gibberellin, jasmonic acid, and auxin were related to male sterility. The results obtained in this study provide insights into the molecular mechanism responsible for male sterility and fertility in pepper.

Morphological characteristics and transcriptome analysis at different anther development stages of the male sterile mutant MS7-2 in Wucai (Brassica campestris L.)

BACKGROUND

The discovery of male sterile materials is of great significance for the development of plant fertility research. Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a variety of non-heading Chinese cabbage. There are few studies on the male sterility of wucai, and the mechanism of male sterility is not clear. In this study, the male sterile mutant MS7-2 and the wild-type fertile plant MF7-2 were studied.

RESULTS

Phenotypic characteristics and cytological analysis showed that MS7-2 abortion occurred at the tetrad period. The content of related sugars in the flower buds of MS7-2 was significantly lower than that of MF7-2, and a large amount of reactive oxygen species (ROS) was accumulated. Through transcriptome sequencing of MS7-2 and MF7-2 flower buds at three different developmental stages (a-c), 2865, 3847, and 4981 differentially expressed genes were identified in MS7-2 at the flower bud development stage, stage c, and stage e, respectively, compared with MF7-2. Many of these genes were enriched in carbohydrate metabolism, phenylpropanoid metabolism, and oxidative phosphorylation, and most of them were down-regulated in MS7-2. The down-regulation of genes involved in carbohydrate and secondary metabolite synthesis as well as the accumulation of ROS in MS7-2 led to pollen abortion in MS7-2.

CONCLUSIONS

This study helps elucidate the mechanism of anther abortion in wucai, providing a basis for further research on the molecular regulatory mechanisms of male sterility and the screening and cloning of key genes in wucai.

Dimethyl phthalate damages Staphylococcus aureus by changing the cell structure, inducing oxidative stress and inhibiting energy metabolism

Dimethyl phthalate (DMP), used as a plasticizer in industrial products, exists widely in air, water and soil. Staphylococcus aureus is a typical model organism representing Gram-positive bacteria. The molecular mechanisms of DMP toxicology in S. aureus were researched by proteomic and transcriptomic analyses. The results showed that the cell wall, membrane and cell surface characteristics were damaged and the growth was inhibited in S. aureus by DMP. Oxidative stress was induced by DMP in S. aureus. The activities of succinic dehydrogenase (SDH) and ATPase were changed by DMP, which could impact energy metabolism. Based on proteomic and transcriptomic analyses, the oxidative phosphorylation pathway was enhanced and the glycolysis/gluconeogenesis and pentose phosphate pathways were inhibited in S. aureus exposed to DMP. The results of real-time reverse transcription quantitative PCR (RT-qPCR) further confirmed the results of the proteomic and transcriptomic analyses. Lactic acid, pyruvic acid and glucose were reduced by DMP in S. aureus, which suggested that DMP could inhibit energy metabolism. The results indicated that DMP damaged the cell wall and membrane, induced oxidative stress, and inhibited energy metabolism and activation in S. aureus.

Integrated Methylome and Transcriptome Analyses Reveal the Molecular Mechanism by Which DNA Methylation Regulates Kenaf Flowering

DNA methylation regulates key biological processes in plants. In this study, kenaf seedlings were pretreated with the DNA methylation inhibitor 5-azacytidine (5-azaC) (at concentrations of 0, 100, 200, 400, and 600 μM), and the results showed that pretreatment with 200 μM 5-azaC promoted flowering most effectively. To elucidate the underlying mechanism, phytohormone, adenosine triphosphate (ATP), and starch contents were determined, and genome-wide DNA methylation and transcriptome analyses were performed on anthers pretreated with 200 μM 5-azaC (5-azaC200) or with no 5-azaC (control conditions; 5-azaC0). Biochemical analysis revealed that 5-azaC pretreatment significantly reduced indoleacetic acid (IAA) and gibberellic acid (GA) contents and significantly increased abscisic acid (ABA) and ATP contents. The starch contents significantly increased in response to 200 and 600 μM 5-azaC. Further genome-wide DNA methylation analysis revealed 451 differentially methylated genes (DMGs) with 209 up- and 242 downregulated genes. Transcriptome analysis showed 3,986 differentially expressed genes (DEGs), with 2,171 up- and 1,815 downregulated genes. Integrated genome-wide DNA methylation and transcriptome analyses revealed 72 genes that were both differentially methylated and differentially expressed. These genes, which included ARFs, PP2C, starch synthase, FLC, PIF1, AGL80, and WRKY32, are involved mainly in plant hormone signal transduction, starch and sucrose metabolism, and flowering regulation and may be involved in early flowering. This study serves as a reference and theoretical basis for kenaf production and provides insights into the effects of DNA methylation on plant growth and development.

Morphological observation and protein expression of fertile and abortive ovules in Castanea mollissima

Chinese chestnuts (Castanea mollissima Blume.) contain 12-18 ovules in one ovary, but only one ovule develops into a seed, indicating a high ovule abortion rate. In this study, the Chinese chestnut 'Huaihuang' was used to explore the possible mechanisms of ovule abortion with respect to morphology and proteomics. The morphology and microstructure of abortive ovules were found to be considerably different from those of fertile ovules at 20 days after anthesis (20 DAA). The fertile ovules had completely formed tissues, such as the embryo sac, embryo and endosperm. By contrast, in the abortive ovules, there were no embryo sacs, and wide spaces between the integuments were observed, with few nucelli. Fluorescence labelling of the nuclei and transmission electron microscopy (TEM) observations showed that cells of abortive ovules were abnormally shaped and had thickened cell walls, folded cell membranes, condensed cytoplasm, ruptured nuclear membranes, degraded nucleoli and reduced mitochondria. The iTRAQ (isobaric tag for relative and absolute quantitation) results showed that in the abortive ovules, low levels of soluble protein with small molecular weights were found, and most of differently expressed proteins (DEPs) were related to protein synthesis, accumulation of active oxygen free radical, energy synthesis and so on. These DEPs might be associated with abnormal ovules formation.

Dynamic expression of miRNAs and functional analysis of target genes involved in the response to male sterility of the wheat line YS3038

Thermosensitive cytoplasmic male sterile (TCMS) lines play an important role in wheat breeding, heterosis utilization, and germplasm innovation. MicroRNAs (miRNAs) can regulate the expression level of target genes by inhibiting the translation of these genes. YS3038 is a wheat TCMS line. In this study, the fertility conversion mechanism of YS3038 was studied by examining the abortion characteristics of YS3038, the regulation pattern of miRNAs and the target genes of miRNAs in YS3038. MiRNA-seq was performed on three important stages of YS3038 under sterile and fertile conditions. Then, the clean reads were aligned with some databases to filter other ncRNAs and repeats. The known miRNAs and novel miRNAs were predicted by sequence comparison with known miRNAs from miRbase. Differential expression of miRNAs between different stages and between different fertile conditions was analyzed, and functional analysis of target genes with opposite expression patterns as those of the miRNAs was conducted. The Ubisch bodies and microspores of sterile anthers were covered with filamentous materials. The degradation of the tapetum cells, the chloroplast structure of endothecium cells, and the microspore structure were abnormal. Microspore development was hindered from the late uninucleate stage to the binucleate stage. Twenty, 52, and 68 differentially expressed miRNAs (DEmiRs) were identified at the early uninucleate, late uninucleate, and binucleate stages, respectively, and there were 0, 7, and 72 differentially expressed target genes (DETGs), respectively, at these three stages. At the binucleate stage, 29 DEmiRs had 41 target mRNAs in total, and the expression patterns of the 41 target mRNAs were opposite to those of the 29 miRNAs. Fifteen significantly enriched KEGG pathways were associated with the 41 target mRNAs. Leucine-rich repeat receptor-like kinases (LRR-RLKs) play important roles in plant developmental and physiological processes. Some studies have shown that the expression of LRR-RLKs is related to the differentiation of microsporocytes and tapetum cells and to male sterility. An LRR-RLK (TaeRPK) gene was silenced by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method, and the seed setting rates of the TaeRPK-silenced plants (3.51%) were significantly lower than those of the negative control plants (88.78%) (P < 0.01). Thus, the TaeRPK gene is likely to be involved in the fertility conversion of YS3038.

Proteomic reveals the influences of smoke-water and karrikinolide on the biosynthesis of salvianolic acids and lignins in Salvia miltiorrhiza hairy roots

The proteins related to the biosynthesis of salvianolic acids and lignins were regulated by smoke-water and karrikinolide in Salvia miltiorrhiza hairy roots. The effects of smoke-water (SW) and karrikinolide (KAR₁) on the biosynthesis of salvianolic acids and lignins in Salvia miltiorrhiza hairy roots have been studied using proteomic technology. The results showed that a total of 1290 and 1678 differentially expressed proteins were respectively obtained in SW and KAR₁ comparing to the control. Bioinformatics analysis indicated the differentially expressed proteins responding to SW and KAR₁ treatments mainly involved in macromolecule metabolic process, cell part, binding, etc., and most of the proteins were located at the cytoplasm and cell membrane, followed by nuclear. In addition, the proteins involved in salvianolic acids biosynthesis were up-regulated, including 4-coumarate-CoA ligase (EC 6.2.1.12) and shikimate O-hydroxycinnamoyl-transferase (EC 2.3.1.133). Enzymes involved in lignins biosynthesis were also identified, e.g. cinnamyl-alcohol dehydrogenase (EC 1.1.1.195) and peroxidase (EC 1.11.1.7). The results indicated that proteins related to the biosynthesis of salvianolic acids and lignins were regulated by SW and KAR₁ in S. miltiorrhiza hairy roots. This study will enhance our understanding of the mechanism by which SW and KAR₁ on the biosynthesis of salvianolic acids and lignins in S. miltiorrhiza hairy roots.

Reactive Oxygen Species Accumulation Strongly Allied with Genetic Male Sterility Convertible to Cytoplasmic Male Sterility in Kenaf

Male sterility (MS) plays a key role in the hybrid breed production of plants. Researchers have focused on the association between genetic male sterility (GMS) and cytoplasmic male sterility (CMS) in kenaf. In this study, P9BS (a natural GMS mutant of the kenaf line P9B) and male plants of P9B were used as parents in multiple backcross generations to produce P9SA, a CMS line with stable sterility, to explore the molecular mechanisms of the association between GMS and CMS. The anthers of the maintainer (P9B), GMS (P9BS), and CMS (P9SA) lines were compared through phenotypic, cell morphological, physiological, biochemical observations, and transcriptome analysis. Premature degradation of the tapetum was observed at the mononuclear stage in P9BS and P9SA, which also had lower activity of reactive oxygen species (ROS) scavenging enzymes compared with P9B. Many coexpressed differentially expressed genes were related to ROS balance, including ATP synthase, electron chain transfer, and ROS scavenging processes were upregulated in P9B. CMS plants had a higher ROS accumulation than GMS plants. The MDA content in P9SA was 3.2 times that of P9BS, and therefore, a higher degree of abortion occurred in P9SA, which may indicate that the conversion between CMS and GMS is related to intracellular ROS accumulation. Our study adds new insights into the natural transformation of GMS and CMS in plants in general and kenaf in particular.

Quantitative Proteome Profiling Provides Insight into the Proteins Associated with β-Glucan Accumulation in Hull-less Barley Grains

The hull-less barley (Qingke) is widely planted as a staple food crop in the Tibetan area, China, and the grains contains high content of β-glucan (BG). The mechanisms of BG synthesis and accumulation in qingke has not been studied at the protein level. This study characterized the proteins associated with BG synthesis and accumulation during qingke seed development. The proteome profiles of qingke seeds taken at 20, 30, and 40 days after flowering were compared using the TMT-based quantitative proteomics. A total of 4283 proteins were identified, with 759 being differentially expressed (DEPs) throughout seed development. Comparisons of protein expression pattern, functions, and pathway enrichment tests highlight cell wall modification, carbon and energy metabolism, polysaccharide metabolism, post-transcriptional modifications, and vesicular transport as critical biological processes related to qingke BG accumulation. Furthermore, induction of starch synthase, starch branching enzyme, pectin acetyl esterases, beta-glucosidases, beta-amylases, 1,4-beta-xylan, xyloglucan, α-amylase inhibitors, and glycosyltransferases underpinned BG synthesis. The results also indicated that the proteins involved in glycolytic, gluconeogenesis, and glyoxylate bypass pathways provided energy and reducing power for BG storage. Parallel reaction monitoring (PRM) and quantitative real-time PCR (qPCR) analyses confirmed the expression profile of the proteins obtained by TMT-based proteomics. The current results provided an insight into the mechanisms of BG synthesis and accumulation during qingke seed development.

Full-length transcriptome analysis reveals the differences between floral buds of recessive genic male-sterile line (RMS3185A) and fertile line (RMS3185B) of cabbage

Starch and sucrose metabolism and plant-pathogen interaction pathways play a dominate role in recessive genic male sterility (RGMS) of cabbage (Brassica oleracea L. var. capitata). RGMS is common in plants and has been widely applied as an effective and economic system for hybrid seed production in many crops. However, little is known regarding the molecular mechanisms of RGMS in cabbage. Hence, full-length transcriptomic and physiological analysis were performed in the spontaneous RGMS mutant RMS3185A and its near-isogenic fertile line (NIL) RMS3185B of small (< 1.6 mm in diameter), medium (~ 2.5 mm in diameter), and large floral buds (~ 3.4 mm in diameter) to identify the differentially expressed genes (DEGs) associated with RMGS. The pollen abnormalities between RMS3185B and RMS3185A appeared at the large floral bud stage. In contrast with RMS3185B, the mature anthers and stamens of RMS3185A were shorter than those of RMS3185B, and the anthers did not dehiscent. The concentrations of glucose, fructose, trehalose, starch, and cellulose in RMS3185A were all significantly lower than those in large floral buds of RMS3185B. PacBio sequencing results showed that DEGs were mainly concentrated in large floral bud stage. In combination with the KEGG enrichment analysis of DEGs in GO terms related to cell wall, pollen and anther, pentose and glucuronate interconversions (ko00040), starch and sucrose metabolism (ko00500), and plant-pathogen interaction (ko04626) were significantly enriched. Among which, cell-wall/pectin-related genes of eighteen PEI, twenty-two PEL, three PG, and fifteen PGL involved in ko00040, and one UGDH, one SPS, four CWINV, four TPP/TPS, and four EGL involved in ko00500, as well as plant-pathogen interaction genes, including sixteen calcium-dependent protein kinase (CDPK), one cyclic nucleotide-gated ion channel (CNGC), and twenty-three calcium-binding protein CML (CML), were significantly down-regulated in RMS3185A relative to that in RMS3185B. Besides, genes involved in ko04626, including two CML and one transcription factor WRKY33, were up-regulated in RMS3185A relative to that in RMS3185B. In conclusion, we hypothesized that the expression alterations of these genes were responsible for calcium signaling and sugar metabolism, thus affecting the occurrence of RGMS in cabbage.

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.

Dibutyl phthalate contamination accelerates the uptake and metabolism of sugars by microbes in black soil

Dibutyl phthalate (DBP) is widely used as plasticizer and has been detected in the environment, posing a threat to animal health. However, the effects of DBP on agricultural microbiomes are not known. In this study, DBP levels in black soil were evaluated, and the impact of DBP contamination on the uptake and metabolism of sugars in microbes was assessed by glucose absorption tests, metaproteomics, metabolomics, enzyme activity assays and computational simulation analysis. The results indicated that DBP contamination accelerated glucose consumption and upregulated the expression of porins and periplasmic monosaccharide ATP-binding cassette (ABC) transporter solute-binding proteins (SBPs). DBP and its metabolic intermediates (carboxymuconate and butanol) may form a stable complex with sugar transporters and enhance the rigidity and stability of these proteins. Sugar metabolism resulting in the generation of ATP and reducing agent (NADPH), as well as the expression of some key enzymes (dehydrogenases) were also upregulated by DBP treatment. Moreover, a diverse bacterial community appears to utilize sugar, suggesting that there are widespread effects of DBP contamination on soil microbial ecosystems. The results of this study provide a theoretical basis for investigating the toxicological effects of DBP on microbes in black soil.

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.

Proteomic variations after short-term heat shock treatment reveal differentially expressed proteins involved in early microspore embryogenesis in cabbage (Brassica oleracea)

Microspore embryogenesis (ME), a widely used haploid breeding method that can considerably shorten the breeding cycle, provides an efficient mean of cultivating many important Brassica crops, such as cabbage, Chinese cabbage, and oilseed rape. For cabbage, in many cases, short-term heat shock treatment can strongly increase the embryogenesis rate, however, the underlying mechanism of this effect has not been elucidated. In this study, we compared the proteomics of isolated microspores with samples pretreated at 32 °C for 24 h and 25 °C for 24 h using two cabbage accessions (Zhonggan 628 and 87–534) showing highly different embryogenic rates. The embryo yield was 19.7 embryos/bud in Zhonggan 628 after 32 °C treatment, while no embryoid was observed in Zhonggan 628 after 25 °C treatment as well as in 87–534 at both temperatures. We identified a total of 363 and 282 differentially expressed proteins (DEPs) for Zhonggan 628 and 87–534 via a label-free proteomics technology. There were 97 DEPs specifically identified only in Zhonggan 628 but not in 87–534 after 32 °C heat-shock treatment that may be related to heat shock-induced embryogenesis in vitro culture. These DEPs were primarily enriched in carbon metabolic process, protein synthesis and degradation process, and signal transduction. Based on protein-protein interaction and pathway enrichment analyses, we proposed that SGT1 homolog A and B(SGT1), heat shock 70 kDa protein 5 (HSP70), cell division control protein 48 homolog A (CDC48) and fatty acyl-CoA reductase (FAR) might play important roles in microspore embryogenesis. This proteomic study may contribute to our molecular understanding of cabbage microspore embryogenesis and help to build a high-efficiency haploid breeding system.

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.

Blocked synthesis of sporopollenin and jasmonic acid leads to pollen wall defects and anther indehiscence in genic male sterile wheat line 4110S at high temperatures

Environment-sensitive genic male sterility is a valid tool for hybrid production and hybrid breeding, but there are no previous reports of the molecular mechanism of fertility conversion. In this study, RNA-seq, phenotypic and cytological observations, and physiological indexes were applied to analyze thermo-sensitive genic male sterility line 4110S under different temperature conditions to explore the fertility transformation mechanism. In total, 3420 differentially expressed genes (DEGs) were identified comprising 2331 upregulated genes and 1089 downregulated genes. The DEGs were apparently distributed among 54 Gene Ontology functional groups. The phenylpropanoid, long-chain fatty acid, and jasmonic acid (JA) biosynthesis pathways were related to male sterility, where their downregulation blocked the synthesis of sporopollenin and JA. Phenotypic and cytological analyses showed that pollen wall defects and anther indehiscence at high temperatures induced sterility. Moreover, enzyme-linked immunosorbent assay results indicated that the abundance of JA was lower in 4110S under restrictive conditions (high temperature) than permissive conditions (low temperature). A possible regulated network of pathways associated with male sterility was suggested. These results provided insights into the molecular mechanism of fertility conversion in the thermosensitive male sterility system.

Comparative Transcriptome Analysis Reveals the Cause for Accumulation of Reactive Oxygen Species During Pollen Abortion in Cytoplasmic Male-Sterile Kenaf Line 722HA

Cytoplasmic male sterility (CMS) is a maternally inherited trait used for hybrid production in plants, a novel kenaf CMS line 722HA was derived from the thermo-sensitive male-sterile mutant ‘HMS’ by recurrent backcrossing with 722HB. The line 722HA has great potential for hybrid breeding in kenaf. However, the underlying molecular mechanism that controls pollen abortion in 722HA remains unclear, thus limiting the full utilization of this line. To understand the possible mechanism governing pollen abortion in 722HA, cytological, transcriptomic, and biochemical analyses were carried out to compare the CMS line 722HA and its maintainer line 722HB. Cytological observations of the microspore development revealed premature degradation of the tapetum at the mononuclear stage, which resulted in pollen dysfunction. The k-means clustering analysis of differentially expressed genes (DEGs) revealed that these genes are related to processes associated with the accumulation of reactive oxygen species (ROS), including electron transport chain, F₁F₀-ATPase proton transport, positive regulation of superoxide dismutase (SOD), hydrogen peroxide catabolic, and oxidation-reduction. Biochemical analysis indicated that ROS-scavenging capability was lower in 722HA than in 722HB, resulting in an accumulation of excess ROS, which is consistent with the transcriptome results. Taken together, these results demonstrate that excessive ROS accumulation may affect the normal development of microspores. Our study provides new insight into the molecular mechanism of pollen abortion in 722HA and will promote further studies of kenaf hybrids.

Analysis of metabolic pathways related to fertility restoration and identification of fertility candidate genes associated with Aegilops kotschyi cytoplasm in wheat (Triticum aestivum L.)

BACKGROUND

Thermo-sensitive male-sterility based on Aegilops kotschyi cytoplasm (K-TCMS) plays an important role in hybrid wheat breeding. This has important possible applications in two-line hybrid wheat breeding but the genetic basis and molecular regulation mechanism related to fertility restoration are poorly understood. In this study, comparative transcriptome profiling based on RNA sequencing was conducted for two near-isogenic lines comprising KTM3315R and its sterile counterpart KTM3315A, a total of six samples (3 repetitions per group), in order to identify fertility restoration genes and their metabolic pathways.

RESULTS

In total, 2642 significant differentially expressed genes (DEGs) were detected, among which 1238 were down-regulated and 1404 were up-regulated in fertile anthers. Functional annotation enrichment analysis identified important pathways related to fertility restoration, such as carbohydrate metabolism, phenylpropanoid metabolism and biosynthesis, as well as candidate genes encoding pectin methylesterase and flavanone 3-hydroxylase. Moreover, transcription factor analysis showed that a large number of DEGs were mainly involved with the WRKY, bHLH, and MYB transcription factor families. Determination of total soluble sugar and flavonoid contents demonstrated that important metabolic pathways and candidate genes are associated with fertility restoration. Twelve DEGs were selected and detected by quantitative reverse-transcribed PCR, and the results indicated that the transcriptome sequencing results were reliable.

CONCLUSIONS

Our results indicate that identified DEGs were related to the fertility restoration and they proved to be crucial in Aegilops kotschyi cytoplasm. These findings also provide a basis for exploring the molecular regulation mechanism associated with wheat fertility restoration as well as screening and cloning related genes.

Theoretical Investigation of the Topology of Spiroborate-Linked Ionic Covalent Organic Frameworks (ICOFs)

A novel type of ionic covalent organic framework (ICOF) with a spiroborate linkage has been recently designed and synthesized by Zhang and co-workers (Ionic Covalent Organic Frameworks with Spiroborate Linkage, Angew. Chem. Int. Ed. 2016, 55, 1737-1741). The spiroborate-linked ICOFs exhibit high Brunauer-Emmett-Teller (BET) surface areas and significant amounts of H₂ and CH₄ uptakes, combined with excellent thermal and chemical stabilities. Inspired by the novel properties of ICOFs, with the aim of gaining better understanding of the structure of such spiroborate-linked ICOFs, a series of potential 3D network configurations of ICOFs connected with tetrahedral [BO₄ ]^- nodes were proposed, assuming the [BO₄ ]^- node in spiroborate segments takes a tetrahedral configuration. These ICOFs, in terms of 2D and 3D topology through torsional energy of the [BO₄ ]^- fragment, pore-size distribution, total energy of the framework, and gas adsorption properties were compared and systematically investigated by density functional theory calculations, molecular mechanics, and well-established Grand canonical Monte Carlo simulations. The results indicate that spiroborate-linked ICOFs are likely a mixture of various topologies. Among these architectures, the five-fold interpenetrating model shows the lowest energy and reasonable gas uptakes, therefore, it is considered to be the most possible structure. More importantly, the five-fold interpenetrating model, showing high CH₄ uptakes compared with several classic porous materials, represents a promising CH₄ storage material.

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.