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

Zhou, Xue; Shi, Fengyan; Zhou, Li; Zhou, Yu; Liu, Zhiyong; Ji, Ruiqin; Feng, Hui

doi:10.1016/j.jprot.2019.103395

Cited by 22 publications

(25 citation statements)

References 53 publications

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“…In Cucumis sativus, the DEGs were mainly enriched in the pathway of starch and sucrose metabolism in the induction of female flower [70]. Furthermore, proteomic analysis of fertile and sterile flower buds found that the up-and downregulated proteins were mainly involved in starch and sucrose metabolism in Brassica campestris [71]. In Hemerocallis hybrid, quantitative proteomic analysis showed DAPs were mainly enriched in starch and sucrose metabolism during flower development [72].…”

Section: Key Degs and Daps Involved In Starch And Sucrose Metabolism mentioning

confidence: 99%

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

Jing

Chen

et al. 2020

IJMS

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

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Section: Key Degs and Daps Involved In Starch And Sucrose Metabolism mentioning

confidence: 99%

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

Jing

Chen

et al. 2020

IJMS

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“…For example, they can play a role in the regulation of cell apoptosis, proliferation, development, and malignant transformation by participating in transcription, RNA processing, DNA repair and replication (38) . Zhou et al found that the ribosome proteins were essential for anther development and male sterility in sterile buds when they studied genetic male sterile line ‘AB01’ in Chinese cabbage (5) . This study indicates that there is a certain relationship between ribosomal protein and plant male sterility.…”

Section: The Complementarity Of Transcriptomics and Proteomicsmentioning

confidence: 99%

“…In recent years, advancement in molecular technology, has enabled breeders and molecular researchers to identify various plant transcription factors, genes and explore protein expression at the translational, transcriptome and proteome level, such as the CMS studies of the Chinese cabbage (5) , turnip (6) , Cucumis melo L. (7) , cotton (8, 9) , rice (10) , Brassica napus L. (11) . Transcriptomic analysis in cotton (CMS-D8) revealed that the reactive oxygen species (ROS) were released from mitochondria and served as important signal molecules in the nucleus, causing the formation of abnormal tapetum (8) .…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and Proteomic Analyses of a New Cytoplasmic Male Sterile Line with wildGossypium bickii.Genetic Background

Zhao

Wang

et al. 2020

Preprint

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39Cotton is an important fiber crop but has serious effects of heterosis, in which cytoplasmic male 40 sterility (CMS) being the major cause of heterosis in plants. However, there are no studies done on 41 CMS Yamian A in cotton with the genetic background of the Australian wild Gossypium bickii. 42 Transcriptomic and proteomic results showed that UDP-glucosyltransferase -in the nucleus, 60S 43 ribosomal protein L13a-in the cytoplasm, ribulose-1,5-bisphosphate carboxylase/oxygenase -in the 44 chloroplast, glutathione S-transferase -in the cytoplasm, and ATP synthase F1 subunit 1 -in the 45 mitochondrion were upregulated; while low molecular weight heat shock protein -in the chloroplast 46 and ATP synthase D chain-in the mitochondrion were down-regulated expression at the microspore 47 58 Cotton is an important cash crop with high-quality fiber, edible oil, and protein which is mainly 59 used as animal feeds (1) . Heterosis in cotton is quite apparent and has been widely used in yield quality, 60 and resistance studies in cotton (2) . The adoption of the production of hybrid seeds is the most 61 important link among some links of cotton heterosis use. At present, the castration in the production 62 of hybrid seeds often relies on hand emasculation and male-sterile lines including chemically induced 63 male sterility (IMS), genic male sterility (GMS), and cytoplasmic male sterility (CMS) (3) . The 64 production practice showed that CMS is an effective way of heterosis utilization in crop and widely 65 used to produce hybrid seeds, because it eliminates the need for artificial emasculation, saves 66 manpower and material resources, enhance the purity of hybrid seeds and increases the output of 67 crops (3, 4) . All over the world, cotton studies started in the 1960s, since then a number of germplasms 68 have been developed, such as G. arboreum L, G. harknessii Brandegee, G. trilobum (DC.) Skov., G. 69 hirsutum, G. barbadense L., among others. However, there is no report on CMS in cotton with 70 genetic background of Australian wild Gossypium bickii, which has been reported despite the 71 enormous effects of heterosis in cotton germplasm development. 72 In recent years, advancement in molecular technology, has enabled breeders and molecular 73 researchers to identify various plant transcription factors, genes and explore protein expression at the 74 translational, transcriptome and proteome level, such as the CMS studies of the Chinese cabbage (5) , 75 turnip (6) , Cucumis melo L. (7) , cotton (8,9) , rice (10) , Brassica napus L. (11) . Transcriptomic analysis in 76 5 cotton (CMS-D8) revealed that the reactive oxygen species (ROS) were released from mitochondria 77 and served as important signal molecules in the nucleus, causing the formation of abnormal 78 tapetum (8) . Proteome analyses in cotton indicated that the differentially expressed proteins (DEPs) 79 mainly involved in pyruvate, carbohydrate and fatty acid metabolism had been identified between the 80 male-sterile line 1355A a...

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“…First-strand cDNA was further synthesized by a RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, USA). To normalize the expression data, the Actin gene (glyceraldehyde-3-phosphate dehydrogenase, GAPDH) was used as an internal reference, and primer pairs for amplification of the selected genes were designed through Primer 5.0 software (Premier Biosoft, USA) [36,37]. The qRT-PCR assay was carried out with ChamQ TM Universal SYBR 1 Qpcr Master Mix (Vazyme Biotech, China) on an Applied Biosystems StepOnePlus TM (Thermo Fisher Scientific, USA), using the following program: 95˚C for 30 s, followed by 40 cycles of 95˚C for 10 s, and then 60˚C for 30 s. The relative expression levels of target genes were calculated with the 2 -ΔΔCt method [38].…”

Section: Qrt-pcr Assaymentioning

confidence: 99%

“…However, the abundance level of protein species commonly depends on non-coding RNAs, mutation, degradation, protein interaction, post-translational modification, and DNA methylation [42,43]. Actually, a combined transcriptomic and proteomic analysis could indicate a reference catalog with great contiguity, wholeness, and accuracy for researchers and could provide an efficient way to understand how transcribed mRNA is manifested at the protein level [37].…”

Section: Annotation and Network Analyses Of Genes And Proteins Providmentioning

confidence: 99%

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

Muhammad

et al. 2020

PLoS ONE

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

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

Cited by 22 publications

References 53 publications

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

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

Transcriptomic and Proteomic Analyses of a New Cytoplasmic Male Sterile Line with wildGossypium bickii.Genetic Background

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

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