Transcriptomic and proteomic analyses provide new insights into the regulation mechanism of low-temperature-induced leafy head formation in Chinese cabbage

Zhang, Changwei; Wei, Yanping; Xiao, Dong; Gao, Liwei; Lyu, Shanwu; Hou, Xilin; Bouuema, Guusje

doi:10.1016/j.jprot.2016.05.022

Cited by 35 publications

(22 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…6C, lanes 7 and 9, respectively) were used. All mass and molar ratios of CFH to FHR1 used are in agreement with the majority of physiological ratios reported (36,(38)(39)(40)(41)(42). Independent of the concentrations used, cofactor activity for FI was not observed for FHR1 alone (Fig.…”

Section: A Gwas Reveals a Cluster Of Genetic Variants Within Cfhr Gensupporting

confidence: 84%

A genome-wide association study identifies key modulators of complement factor H binding to malondialdehyde-epitopes

Alic

Papac-Miličević

Rudnick

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Genetic variants within complement factor H (CFH), a major alternative complement pathway regulator, are associated with the development of age-related macular degeneration (AMD) and other complementopathies. This is explained with the reduced binding of CFH or its splice variant factor H-like protein 1 (FHL-1) to self-ligands or altered self-ligands (e.g., malondialdehyde [MDA]-modified molecules) involved in homeostasis, thereby causing impaired complement regulation. Considering the critical role of CFH in inhibiting alternative pathway activation on MDA-modified surfaces, we performed an unbiased genome-wide search for genetic variants that modify the ability of plasma CFH to bind MDA in 1,830 individuals and characterized the mechanistic basis and the functional consequences of this. In a cohort of healthy individuals, we identified rs1061170 in CFH and the deletion of CFHR3 and CFHR1 as dominant genetic variants that modify CFH/FHL-1 binding to MDA. We further demonstrated that FHR1 and FHR3 compete with CFH for binding to MDA-epitopes and that FHR1 displays the highest affinity toward MDA-epitopes compared to CFH and FHR3. Moreover, FHR1 bound to MDA-rich areas on necrotic cells and prevented CFH from mediating its cofactor activity on MDA-modified surfaces, resulting in enhanced complement activation. These findings provide a mechanistic explanation as to why the deletion of CFHR3 and CFHR1 is protective in AMD and highlight the importance of genetic variants within the CFH/CFHR3/CFHR1 locus in the recognition of altered-self in tissue homeostasis.

show abstract

Section: A Gwas Reveals a Cluster Of Genetic Variants Within Cfhr Gensupporting

confidence: 84%

A genome-wide association study identifies key modulators of complement factor H binding to malondialdehyde-epitopes

Alic

Papac-Miličević

Rudnick

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Furthermore, the differential expression of BrCML genes related to the formation of leafy-head in response to low temperature was analysed. The transcriptomic data of Chinese cabbage inbred line ‘Chiifu-402’ were retrieved from a previous report concerning low-temperature induced leafy-head formation [ 31 ]. Consequently, 54 differentially expressed BrCML genes were detected between the heading group (a constant 25 °C temperature) and non-heading group (a 4 °C low temperature treatment) (Additional file 8 : Figure S3; Additional file 9 : Table S6).…”

Section: Resultsmentioning

confidence: 99%

Genome-wide identification and expression analysis of calmodulin-like (CML) genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Nie

Zhang

2017

BMC Genomics

View full text Add to dashboard Cite

BackgroundCalmodulin-like (CML) proteins are a primary family of plant-specific Ca2+ sensors that specifically bind to Ca2+ and deliver a Ca2+ signal. CML proteins have been identified and characterized in many plant species, such as the model plant Arabidopsis and rice. Based on considerable evidence, the roles of CML proteins are crucial in plant growth and development and in the response to various external stimuli. Nevertheless, the characterization and expression profiling of CML genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis) remain limited.ResultsIn this study, a genome-wide search and comprehensive analysis were performed, and a total of 79 BrCML genes were identified in Chinese cabbage. Gene structure analysis revealed that these BrCML genes contained two to four conserved EF-hand motifs. Phylogenetic analysis showed that CML homologs between Chinese cabbage and Arabidopsis shared close relationships. The identified BrCML genes were located across ten chromosomes and three different subgenomes of Chinese cabbage. Moreover, 126 pairs of orthologous CML genes were found among Chinese cabbage, Arabidopsis and Brassica oleracea. Expression analysis revealed that the expression of some BrCML genes was tissue-specific and that of some was susceptible to temperature stress. A putative interaction network of BrCML proteins was proposed, which suggested that BrCML2, BrCML6, BrCML15 and BrCML25 were co-expressed and might play roles in flower development and other relevant biological processes of Chinese cabbage.ConclusionsThe results of this study increased the understanding and characterization of BrCML genes in Chinese cabbage, and will be a rich resource for further studies to investigate BrCML protein function in various developmental processes of Chinese cabbage.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4240-2) contains supplementary material, which is available to authorized users.

show abstract

“…Protein-mediated post-transcriptional and post-translational processes result in the final cellular products, compared to genome and transcriptome. 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

View full text Add to dashboard Cite

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.

show abstract

Transcriptomic and proteomic analyses provide new insights into the regulation mechanism of low-temperature-induced leafy head formation in Chinese cabbage

Cited by 35 publications

References 25 publications

A genome-wide association study identifies key modulators of complement factor H binding to malondialdehyde-epitopes

A genome-wide association study identifies key modulators of complement factor H binding to malondialdehyde-epitopes

Genome-wide identification and expression analysis of calmodulin-like (CML) genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

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

Contact Info

Product

Resources

About