Proteomic analysis of protein lysine 2-hydroxyisobutyrylation (Khib) in soybean leaves.

BACKGROUND: Protein lysine 2-hydroxyisobutyrylation (Khib) is a novel post-translational modification (PTM) discovered in cells or tissues of animals, microorganisms and plants in recent years. Proteome-wide identification of Khib-modified proteins has been performed in several plant species, suggesting that Khib-modified proteins are involved in a variety of biological processes and metabolic pathways. However, the protein Khib modification in soybean, a globally important legume crop that provides the rich source of plant protein and oil, remains unclear. RESULTS: In this study, the Khib-modified proteins in soybean leaves were identified for the first time using affinity enrichment and high-resolution mass spectrometry-based proteomic techniques, and a systematic bioinformatics analysis of these Khib-modified proteins was performed. Our results showed that a total of 4251 Khib sites in 1532 proteins were identified as overlapping in three replicates (the raw mass spectrometry data are available via ProteomeXchange with the identifier of PXD03650). These Khib-modified proteins are involved in a wide range of cellular processes, particularly enriched in biosynthesis, central carbon metabolism and photosynthesis, and are widely distributed in subcellular locations, mainly in chloroplasts, cytoplasm and nucleus. In addition, a total of 12 sequence motifs were extracted from all identified Khib peptides, and a basic amino acid residue (K), an acidic amino acid residue (E) and three aliphatic amino acid residues with small side chains (G/A/V) were found to be more preferred around the Khib site. Furthermore, 16 highly-connected clusters of Khib proteins were retrieved from the global PPI network, which suggest that Khib modifications tend to occur in proteins associated with specific functional clusters. CONCLUSIONS: These findings suggest that Khib modification is an abundant and conserved PTM in soybean and that this modification may play an important role in regulating physiological processes in soybean leaves. The Khib proteomic data obtained in this study will help to further elucidate the regulatory mechanisms of Khib modification in soybean in the future.

Maize (Zea mays L.) planted at higher density utilizes dynamic light more efficiently.

In nature, plants are exposed to a dynamic light environment. Fluctuations in light decreased the photosynthetic light utilization efficiency (PLUE) of leaves, and much more severely in C4 species than in C3 species. However, little is known about the plasticity of PLUE under dynamic light in C4 species. Present study focused on the influence of planting density to the photosynthesis under dynamic light in maize (Zea mays L.), a most important C4 crop. In addition, the molecular mechanism behind photosynthetic adaptation to planting density were also explored by quantitative proteomics analysis. Results revealed that as planting density increases, maize leaves receive less light that fluctuates more. The maize planted at high density (HD) improved the PLUE under dynamic light, especially in the middle and later growth stages. Quantitative proteomics analysis showed that the transfer of nitrogen from Rubisco to RuBP regeneration and C4 pathway related enzymes contributes to the photosynthetic adaptation to lower and more fluctuating light environment in HD maize. This study provides potential ways to further improve the light energy utilization efficiency of maize in HD.

Leaf shape, planting density, and nitrogen application affect soybean yield by changing direct and diffuse light distribution in the canopy.

When attempting to maximize the crop yield from field-grown soybean (Glycine max (L.) Merr.) by means of improving the light conditions for photosynthesis in the canopy, it is crucial to find the optimal planting density and nitrogen application rate. The soybean plants that were the subject of our experiment were cultivated in N-dense mutual pairs, and included two cultivars with different leaf shapes; one cultivar sported ovate leaves (O-type) and the other lanceolate leaves (L-type). We analyzed the results quantitatively to determine the amount of spatial variation in light distribution and photosynthetic efficiency across the canopy, and to gauge the effect of the experimental parameters on the yield as well as the photosynthetic light and nitrogen use efficiency of the crop. Results indicate that the different leaf shapes were responsible for significant disparities between the photosynthetic utilization of direct and diffuse light. As the nitrogen fertilizer rate and the planting density increased, the soybean plants responded by adjusting leaf morphology in order to maximize the canopy apparent photosynthetic light use efficiency, which in turn affected the leaf nitrogen distribution in the canopy. Despite the fact that the light interception rate of the canopy of the L-type cultivar was lower than that of the canopy of the O-type cultivar, we found its canopy apparent photosynthetic nitrogen and light use efficiency were higher. It was interesting to note, however, that the nitrogen and light use efficiency contributions associated with exposure to diffuse light were greater for the latter than for the former.