ABSTRACT: De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways
Project description:In this study, we performed de novo transcriptome assembly for L. japonica, representing transcripts from nine different tissues. A total of 22Gbps clean RNA-seq reads from nine tissues of L. japonica were used, resulting in 243,185 unigenes, with 99,938 unigenes annotated based on homology search using blastx against NCBI-nr protein database. Unsupervised principal component analysis and correlation studies using transcripts expression data from all nine tissues of L. japonica showed relationships between tissues explaining their association at different developmental stages. Homologs for all genes associated with chlorogenic acid, luteolin, and secoiridoid biosynthesis pathways were identified in the L. japonica transcriptome assembly. Expression of unigenes associated with chlorogenic acid were enriched in stem and leaf-2, unigenes from luteolin were enriched in stem and flowers, while unigenes from secoiridoid metabolic pathways were enriched in leaf-1 and shoot apex. Our results showed that different tissues of L. japonica are enriched with sets of unigenes associated with a specific pharmaceutically important metabolic pathways, and therefore, possess unique medicinal properties. Present study will serve as a resource for future attempts for functional characterization of enzyme coding genes within key metabolic processes. De novo transcriptome assembly and characterization, and transcriptome profiling for nine tissues of Lonicera japonica
Project description:In this study, we performed de novo transcriptome assembly for L. japonica, representing transcripts from nine different tissues. A total of 22Gbps clean RNA-seq reads from nine tissues of L. japonica were used, resulting in 243,185 unigenes, with 99,938 unigenes annotated based on homology search using blastx against NCBI-nr protein database. Unsupervised principal component analysis and correlation studies using transcripts expression data from all nine tissues of L. japonica showed relationships between tissues explaining their association at different developmental stages. Homologs for all genes associated with chlorogenic acid, luteolin, and secoiridoid biosynthesis pathways were identified in the L. japonica transcriptome assembly. Expression of unigenes associated with chlorogenic acid were enriched in stem and leaf-2, unigenes from luteolin were enriched in stem and flowers, while unigenes from secoiridoid metabolic pathways were enriched in leaf-1 and shoot apex. Our results showed that different tissues of L. japonica are enriched with sets of unigenes associated with a specific pharmaceutically important metabolic pathways, and therefore, possess unique medicinal properties. Present study will serve as a resource for future attempts for functional characterization of enzyme coding genes within key metabolic processes.
Project description:Lonicera japonica Thunb is a typical Chinese medicinal material with the homology of medicine and food. Post-translational modification (PTM) of proteins can significantly affect protein structure and function, and plays a very important regulatory role in plant development. However, to date, little is known about the functions of PTM in L. japonica. Therefore, the study of lysine succinylation during the floral developmental stages will help to understand the mechanism of the secondary metabolism of L. japonica. In this study, we first analyzed lysine succinylation exist in L. japonica, and found lysine succinylation is highly abundant in juvenile bud stage than gold flowering stage. Then a highly efficient enrichment method for succinylation peptides was used to identify 586 succinylation modification sites in 303 proteins in L. japonica. Our bioinformatics analysis further revealed that the succinylated proteins are involved in many important biological processes including TCA, amino acid metabolism and secondary metabolism. With the development of flowering stage of L. japonica, the succinylation degree of aspartate transaminase was up-regulated while 4-coumarate-CoA ligase was down-regulated, suggesting that succinylation of proteins is important for the bioactive compounds’ biosynthesis process in L. japonica. Protein modification in vitro also verified the impact of succinylation on both 4CL and AT enzyme activity would be changed. As a consequence, current examine provides new insight into the molecular mechanism underlying the accumulation of active ingredients in L. japonica at the post-translational modification level.
