Effective protein extraction protocol for proteomics studies of Jerusalem artichoke leaves.

Protein extraction is a crucial step for proteomics studies. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis (2DE) analysis in Jerusalem artichoke (Helianthus tuberosus L.), three different protein extraction methods-trichloroacetic acid/acetone, Mg/NP-40, and phenol/ammonium acetate-were evaluated using Jerusalem artichoke leaves as source materials. Of the three methods, trichloroacetic acid/acetone yielded the best protein separation pattern and highest number of protein spots in 2DE analysis. Proteins highly abundant in leaves, such as Rubisco, are typically problematic during leaf 2DE analysis, however, and this disadvantage was evident using trichloroacetic acid/acetone. To reduce the influence of abundant proteins on the detection of low-abundance proteins, we optimized the trichloroacetic acid/acetone method by incorporating a PEG fractionation approach. After optimization, 363 additional (36.2%) protein spots were detected on the 2DE gel. Our results suggest that trichloroacetic acid/acetone method is a better protein extraction technique than Mg/NP-40 and phenol/ammonium acetate in Jerusalem artichoke leaf 2DE analysis, and that trichloroacetic acid/acetone method combined with PEG fractionation procedure is the most effective approach for leaf 2DE analysis of Jerusalem artichoke.

A Chromosome-Scale Genome Assembly of Paper Mulberry (Broussonetia papyrifera) Provides New Insights into Its Forage and Papermaking Usage.

Paper mulberry (Broussonetia papyrifera) is a well-known woody tree historically used for Cai Lun papermaking, one of the four great inventions of ancient China. More recently, Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents. In this study, we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches, including Illumina and PacBio sequencing platform as well as Hi-C, optical, and genetic maps. The assembled Paper mulberry genome consists of 386.83 Mb, which is close to the estimated size, and 99.25% (383.93 Mb) of the assembly was assigned to 13 pseudochromosomes. Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families, respectively, accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry. Moreover, the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine, forage, papermaking, and barkcloth making. We also identified the root-associated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation. Collectively, these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition. Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making, and as forage. These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide.

Proteomics analysis of rice seedling responses to ovine saliva.

Grazing is accompanied by a multitude of processes including wounding, saliva deposition, and defoliation. Previous studies have focused on the effects of the grazing or clipping intensity on plant regrowth, survival, and composition in the grassland. However, the impact of saliva deposition on plants is poorly understood. In this study, rice was used as a model plant to study the differentially expressed proteins after ovine saliva treatment. The shoots of 2-week-old seedlings were crosscut and the lower parts were daubed with ovine saliva at the cut surface. After 2, 6, 12 and 24h, proteomics analysis was performed using proteins extracted from the saliva-treated shoots. The results showed that proteins involved in multiple pathways were differentially expressed in response to ovine saliva, including catalase (CAT), peroxiredoxin (Prx), ATP synthase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Moreover, real-time quantitative reverse-transcription-PCR (RT-PCR) data showed that most of the genes were also regulated at the transcript level. Our results indicate the ovine saliva induces an early response in the rice seedling by stress-related pathways. This study provides information about the response of rice seedlings to ovine saliva at the protein level.