Comparative Transcriptome and Proteome Analysis Provides New Insights Into the Mechanism of Protein Synthesis in Kenaf (Hibiscus cannabinus L.) Leaves

Abstract

Given the rising domestic demand and increasing global prices of corn and soybean, China is looking for alternatives for these imports to produce animal fodder. Kenaf (Hibiscus cannabinus L.) has great potential as a new forage source, due to abundant proteins, phenols and flavonoids in its leaves. However, few studies have evaluated the mechanism of protein synthesis in kenaf leaves. In the current work, compared with kenaf material “L332,” the percentage of crude protein content in leaves of material “Q303” increased by 6.13%; combined with transcriptome and proteome data, the kenaf samples were systematically studied to obtain mRNA-protein correlation. Then, the genes/proteins related to protein synthesis in the kenaf leaves were obtained. Moreover, this work detected mRNA expression of 20 differentially expressed genes (DEGs). Meanwhile, 20 differentially expressed proteins (DEPs) related to protein synthesis were performed parallel reaction monitoring. Fructose-1,6-bisphosphatase (FBP), nitrite reductase (NirA), prolyl tRNA synthase (PARS) and glycine dehydrogenase (GLDC) presented increased mRNA and protein levels within kenaf leaves with high protein content. Based on the obtained findings, FBP, NirA, PARS, and GLDC genes may exert a vital function in the protein synthesis of kenaf leaves. The results provide a new idea for further studying the potential genes affecting the quality trait of protein content in kenaf leaves and provide gene resources and a theoretical foundation for further cultivating high protein kenaf varieties.

Comparative Transcriptome Analysis Identified Potential Genes and Transcription Factors for Flower Coloration in Kenaf (Hibiscus cannabinus L.)

“…In the present study, using RNA-seq by paired-end sequencing technology performed analyses of the kenaf flower transcriptome. According to RNA-seq data, the three kenaf at two different developmental stages were assembled, resulting in 81,982 total transcripts with an N50 score of 1882 bp; the total was similar to the previous kenaf study [16] or achieved a slightly decreasing assembly level compared with Zhang et al [17]. In the de novo assembly process, assembled transcript quality is more important than the number of generated transcripts.…”

“…Transcriptome analysis by RNA-seq is a useful tool for evaluating gene expression at the mRNA level and provides detailed knowledge for identifying candidate genes of biochemical traits. In kenaf, transcriptome analysis was widely used to develop molecular markers [32][33][34], find putative genes involved in agronomic [35,36] and biochemical traits [17,37], and screen candidate genes involved in stress response [18,38]. However, these studies were conducted using limited tissues including leaf, shoot, and stem.…”

“…Using the PAC-Bio sequencing method, the novel candidate genes were found to be related to the lignin and cellulose biosynthetic pathways in kenaf leaves [15]. Moreover, salinity-responsive genes [16], protein synthesis genes [17], and cadmium-responsive genes [18,19] were explored by transcriptome analysis through RNA-seq methods. However, these studies mainly investigated the roots, stems, and leaves of kenaf, whereas studies on flowers were limited.…”

Genome-Wide Identification and Characterization of miRNAs and Natural Antisense Transcripts Show the Complexity of Gene Regulatory Networks for Secondary Metabolism in Aristolochia contorta

“…A heatmap was generated using TBtools [ 72 ] with the fold change values. For differential expression analysis of miRNAs in four tissues, egdeR was employed with the screening criteria of |log2(FC)| ≥ 1.00 and p -value < 0.05 [ 73 ].…”

Anti- and Pro-Oxidant Properties of Essential Oils against Antimicrobial Resistance

“…Tang and colleagues (2021) identified key metabolic pathways that influenced MRSA activity as discussed in the previous section. Transcriptomic and proteomic profiling is becoming a popular approach that helps to measure gene expression and protein abundance [ 56 ]. Techniques such as two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), stable isotopic labeling method, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) aid in finding the effective interactions of EO constituents with their targets, which are mostly proteins in nature [ 57 ].…”